Alignments for a candidate for adiA in Geobacter lovleyi SZ

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Geobacter lovleyi SZ

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate WP_012469733.1 GLOV_RS08315 arginine decarboxylase

Query= BRENDA::A0A076IP90
         (630 letters)



>NCBI__GCF_000020385.1:WP_012469733.1
          Length = 635

 Score =  595 bits (1534), Expect = e-174
 Identities = 303/634 (47%), Positives = 426/634 (67%), Gaps = 6/634 (0%)

Query: 1   MRKWRIEDSEELYNITGWGTSYFGINDKGHVVVTPRKDGVE-VDLKELVDELQLRDVAAP 59
           M +W I +S ++YN+  WG   F IN KG++ V P  +    +DL+ LVD+L  R +  P
Sbjct: 1   MERWSINESAKVYNLDNWGADLFSINKKGNICVHPSSNSKNAIDLRALVDDLIKRKIKPP 60

Query: 60  MLVRFPDILDNRIEKIANCFKQASDEYGYKAQNFIIYPIKVNQMRPVVEEIISHGKKFNL 119
           +L+RF D+L  RI  I   F+ A  E  Y A+    YPIKVNQ R VVE I S+GK++N+
Sbjct: 61  ILLRFMDVLQGRIASINRVFRNAIAENDYPAKYQTFYPIKVNQQRQVVEAIASYGKRYNI 120

Query: 120 GLEAGSKPELHAVIAVNTDSDSLIICNGYKDESYIELALLAQKMGKRIFLVVEKMNELRL 179
           GLE GSKPEL A IA++T +   IICNGYKD  YIE  L A ++G  I +VVEK+ EL  
Sbjct: 121 GLEVGSKPELVAGIAISTGNGLPIICNGYKDAEYIETVLFATRVGYNITIVVEKLFELEK 180

Query: 180 IAKMAKQLNVRPNIGIRIKLASSGSGKWEDSGGDASKFGLTSSELLEALDFLEKKDMKDC 239
           I ++AK+  +RP++GIR+KL+S G+GKW  SGG+ +KFGL  SE++ A+  L++ D+ DC
Sbjct: 181 IIELAKKTGIRPSLGIRVKLSSKGTGKWATSGGEDAKFGLRMSEIMAAIKMLQEADLLDC 240

Query: 240 LKLIHFHIGSQVTKIRRIKTALREASQFYVQLHVMGFNVEFVDIGGGLGVDYDGTRSANS 299
           + L+H HIGSQVTKI +IKTAL EA++ Y ++  +G N++++DIGGGLGVDYDG++S+  
Sbjct: 241 VNLLHSHIGSQVTKIDKIKTALIEAARIYSEMRKLGVNIQYLDIGGGLGVDYDGSKSSYF 300

Query: 300 ESSVNYSIQEYVNDSISTLVDASDKNGIPHPNIITESGRSLTAHHSVLIFEVLETAT--- 356
            SSVNY+++EY ND I  + +  D+ G+  PNII+ESGR+  AH+SVL+  VL T T   
Sbjct: 301 -SSVNYTVEEYANDVIYQIKNICDEAGVDCPNIISESGRATVAHYSVLVTNVLNTNTQNL 359

Query: 357 LPEMDEDFEVGENDHELVHELYEIWDNLNQSRMVEAWHDAQQIREEALDLFSHGIVDLKT 416
           +P+ ++  E  E     V +L +I+ ++++  + E +HD  Q+  EA+ LF+ G + L+ 
Sbjct: 360 MPDYEQILEEMEKPAPTVKKLLDIYKSIDRYSLREDYHDTLQLINEAVSLFNLGYLTLQD 419

Query: 417 RAQIERLYWSVTREINQIASGLKHAPDEFRKLDKLLADKYFCNFSLFQSLPDSWAIDQIF 476
           RA  E LY  + ++IN I   +K  P+E +     L   YF NFSLFQS+PDSWAIDQ+F
Sbjct: 420 RAIAEWLYSKIIKKINSIVEKIKPIPEELQNFQLALRQTYFANFSLFQSIPDSWAIDQLF 479

Query: 477 PIMPIQRLDEKPDRNATLQDITCDSDGKIANFISTRYVSHDLPVHSLKGKDAYYIGVFLV 536
           PIMP+QRL ++PD  A++ DITCDSDG+I +F+     S  LP+H LK  + YYIG FL+
Sbjct: 480 PIMPLQRLGQRPDVMASIADITCDSDGEITSFVGENGRSKFLPMHKLKKDEDYYIGFFLI 539

Query: 537 GAYQEILGDMHNLFGDTNAVHVTVDDK-GYSIDQVIDGETVAEVLDYVQYNPKKLVRTLE 595
           GAYQEILGD+HNLFGDTNAVH+T + K GY ID VI+G+   E L YVQY   ++++ + 
Sbjct: 540 GAYQEILGDLHNLFGDTNAVHITFNKKTGYMIDTVINGDATWETLKYVQYKGPEILKHVR 599

Query: 596 TWVTKSVKEGRISVEEGKEFLSNYRSGLYGYTYL 629
             + K V   ++S+EE   F+      L GYTYL
Sbjct: 600 DNLEKQVAIKKVSIEESSHFIELLDRTLLGYTYL 633


Lambda     K      H
   0.318    0.136    0.396 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1068
Number of extensions: 44
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 630
Length of database: 635
Length adjustment: 38
Effective length of query: 592
Effective length of database: 597
Effective search space:   353424
Effective search space used:   353424
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate WP_012469733.1 GLOV_RS08315 (arginine decarboxylase)
to HMM TIGR01273 (speA: arginine decarboxylase (EC 4.1.1.19))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01273.hmm
# target sequence database:        /tmp/gapView.16512.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01273  [M=624]
Accession:   TIGR01273
Description: speA: arginine decarboxylase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.3e-266  869.1   0.6   1.1e-265  868.9   0.6    1.0  1  lcl|NCBI__GCF_000020385.1:WP_012469733.1  GLOV_RS08315 arginine decarboxyl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020385.1:WP_012469733.1  GLOV_RS08315 arginine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  868.9   0.6  1.1e-265  1.1e-265       1     623 [.       4     633 ..       4     634 .. 0.98

  Alignments for each domain:
  == domain 1  score: 868.9 bits;  conditional E-value: 1.1e-265
                                 TIGR01273   1 wsaeesakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrFpdilqk 69 
                                               ws++esakvYn+++Wga++f++nk+G+++v+p+ +++++ idl++lv+++ ++++k P+l+rF+d+lq 
  lcl|NCBI__GCF_000020385.1:WP_012469733.1   4 WSINESAKVYNLDNWGADLFSINKKGNICVHPS-SNSKNAIDLRALVDDLIKRKIKPPILLRFMDVLQG 71 
                                               899*****************************7.5569******************************* PP

                                 TIGR01273  70 rikslnaaFkeaieeleYaskyqavyPiKvnqqrevveelvasg.gkslGLEaGsKpEllialalaekp 137
                                               ri+s+n++F++ai e++Y++kyq++yPiKvnqqr+vve++++ g ++++GLE+GsKpEl++++a+++ +
  lcl|NCBI__GCF_000020385.1:WP_012469733.1  72 RIASINRVFRNAIAENDYPAKYQTFYPIKVNQQRQVVEAIASYGkRYNIGLEVGSKPELVAGIAISTGN 140
                                               ********************************************9************************ PP

                                 TIGR01273 138 kavivcnGyKDreyielaliarklglkvviviekleEldlvieeakklgvkPklGlRvrLaskgsgkwa 206
                                               + +i+cnGyKD eyie++l+a+++g++++iv+ekl El+++ie+akk+g++P lG+Rv+L+skg+gkwa
  lcl|NCBI__GCF_000020385.1:WP_012469733.1 141 GLPIICNGYKDAEYIETVLFATRVGYNITIVVEKLFELEKIIELAKKTGIRPSLGIRVKLSSKGTGKWA 209
                                               ********************************************************************* PP

                                 TIGR01273 207 ssgGeksKFGLsasqvlevvkklkeedlldslkllHfHlGsqianiddvkkgvrEaarlyvelrklGvk 275
                                               +sgGe++KFGL++s++++++k l+e+dlld+++llH H+Gsq+++id++k+++ Eaar+y e+rklGv+
  lcl|NCBI__GCF_000020385.1:WP_012469733.1 210 TSGGEDAKFGLRMSEIMAAIKMLQEADLLDCVNLLHSHIGSQVTKIDKIKTALIEAARIYSEMRKLGVN 278
                                               ********************************************************************* PP

                                 TIGR01273 276 ievvdvGGGLgvdYdGtksksdlsvnYsleeyaaavvaalkevceekgvpePviisEsGRaitahhavl 344
                                               i+++d+GGGLgvdYdG+ks++ +svnY++eeya++v++++k++c+e+gv +P+iisEsGRa++ah++vl
  lcl|NCBI__GCF_000020385.1:WP_012469733.1 279 IQYLDIGGGLGVDYDGSKSSYFSSVNYTVEEYANDVIYQIKNICDEAGVDCPNIISESGRATVAHYSVL 347
                                               ********************************************************************* PP

                                 TIGR01273 345 vaevleveeeeeee.aeeile..eeapeevkeleellkeideesaeelledavqlleeavelfklGkld 410
                                               v++vl++++++ ++  e+ile  e+ +++vk+l +++k+id++s++e ++d+ ql++eav+lf+lG+l+
  lcl|NCBI__GCF_000020385.1:WP_012469733.1 348 VTNVLNTNTQNLMPdYEQILEemEKPAPTVKKLLDIYKSIDRYSLREDYHDTLQLINEAVSLFNLGYLT 416
                                               ************9978888886678899***************************************** PP

                                 TIGR01273 411 leeralaeqlalailkkvkeleakekshreildelqeklaekylvnlslFqslPDaWgidqlfPilPle 479
                                               l++ra+ae+l+ +i+kk++++ +k k + e+l+++q  l+++y++n+slFqs+PD+W+idqlfPi+Pl+
  lcl|NCBI__GCF_000020385.1:WP_012469733.1 417 LQDRAIAEWLYSKIIKKINSIVEKIKPIPEELQNFQLALRQTYFANFSLFQSIPDSWAIDQLFPIMPLQ 485
                                               ********************************************************************* PP

                                 TIGR01273 480 rLdekpdrravllDltCDsDGkikkfveeqgiektlplheldkdeeyllgfflvGAYqEiLgdvHnLFg 548
                                               rL ++pd +a+++D+tCDsDG+i++fv+e+g+ k lp+h+l+kde+y++gffl+GAYqEiLgd HnLFg
  lcl|NCBI__GCF_000020385.1:WP_012469733.1 486 RLGQRPDVMASIADITCDSDGEITSFVGENGRSKFLPMHKLKKDEDYYIGFFLIGAYQEILGDLHNLFG 554
                                               ********************************************************************* PP

                                 TIGR01273 549 dteavevvvkekgeveveaieegdtvedvlkavqydpeellkalkqk....vaeaklkaeekkqvlell 613
                                               dt+av++++++k+++ ++++ +gd++++ lk+vqy+  e+lk+++++    va +k++ ee+++++ell
  lcl|NCBI__GCF_000020385.1:WP_012469733.1 555 DTNAVHITFNKKTGYMIDTVINGDATWETLKYVQYKGPEILKHVRDNlekqVAIKKVSIEESSHFIELL 623
                                               ********************************************999877777889************* PP

                                 TIGR01273 614 eaglsgypYL 623
                                               +++l gy+YL
  lcl|NCBI__GCF_000020385.1:WP_012469733.1 624 DRTLLGYTYL 633
                                               *********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (624 nodes)
Target sequences:                          1  (635 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 7.55
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources