GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adiA in Synechococcus elongatus PCC 7942

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate Synpcc7942_1037 Synpcc7942_1037 arginine decarboxylase

Query= BRENDA::P74576
         (695 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_1037 Synpcc7942_1037 arginine
           decarboxylase
          Length = 647

 Score =  843 bits (2178), Expect = 0.0
 Identities = 420/661 (63%), Positives = 514/661 (77%), Gaps = 20/661 (3%)

Query: 28  AGVKTDSNPQAIA-QDRRWTIDDSENLYRITGWGEPYFSINAAGHVTVSPQADHGGALDL 86
           A  +T   P A+A + ++W I+DSE LYRI GWGEPYF INAAGH+TVSPQ D GG+LDL
Sbjct: 2   AAEQTAIAPLAVAVESQQWRIEDSEALYRIQGWGEPYFGINAAGHITVSPQGDRGGSLDL 61

Query: 87  YELVKGLRQRNIGLPLLLRFSDILADRINRLNAAFARGIARYRYPNTYRGVYPIKCNQHR 146
           YELV+ LR+R + LPLL+RF DIL DRI RLNA FA+ IARY Y   YRGV+P+KCNQ R
Sbjct: 62  YELVEALRRRGLNLPLLIRFPDILEDRIERLNACFAKAIARYNYAGEYRGVFPVKCNQQR 121

Query: 147 HIVESLVRYGTPYNFGLEAGSKPELMIALAMLQPQENPEPDQQNQPLLICNGYKDREYIE 206
           H++ESLV YG P+ FGLEAGSKPEL+IALA L              LLICNGYKDR+YIE
Sbjct: 122 HLIESLVNYGRPFQFGLEAGSKPELLIALAHLDTPG---------ALLICNGYKDRDYIE 172

Query: 207 TALLARRLGHRPIIVVEQVAEVALAIEISSNLGIKPILGVRAKLSTQGMGRWGISTGDRA 266
           TA+L RRLG  PI+V+EQ+ EV +AI  S  LGI+PILGVRAKL+ +GMGRWG S GDRA
Sbjct: 173 TAILGRRLGKTPILVIEQLEEVDVAIAASQRLGIEPILGVRAKLNARGMGRWGSSAGDRA 232

Query: 267 KFGLTIPEMLTAIEQLRRADMLDSLQLLHFHIGSQISSISVIKEAMTEASQIFVQLAKLG 326
           KFGLT+PE++ A+E+L+ A++L  LQLLHFHIGSQIS ISV+K+A+ EA+QI+VQLA LG
Sbjct: 233 KFGLTMPEIVAAVEKLQAANLLHCLQLLHFHIGSQISDISVLKDAIQEAAQIYVQLAALG 292

Query: 327 ANMRYLDVGGGLGVDYDGSKTNFYASKNYNIQNYVNDVISAVQDACVAAEVPCPVLISES 386
           A+MRYLDVGGGLGVDYDGSKTNF+ASKNYN+Q Y NDV++ ++DAC A  +  P L SES
Sbjct: 293 ADMRYLDVGGGLGVDYDGSKTNFHASKNYNMQTYANDVVATIKDACQAHRLAVPTLTSES 352

Query: 387 GRAIASHQSVLIFDVVATNDI-NPPLPKVKGKDHAILRNLMETWETITVDNYQEAYHDVE 445
           GRAIASHQSVL+FDV+ ++++    +   + +D AI+R L E  E I ++N QE YHD  
Sbjct: 353 GRAIASHQSVLVFDVLGSSEVPRAAVEPPQEEDSAIVRTLYEVLEAIALENLQECYHDAF 412

Query: 446 QFKTEAISLFNFGYLGLKERAKAEELYWACCRKILQICRQQEYVPDDLENLEVNLASIYY 505
           + K +A+S F  GYL L ERAKAE L+W+CC +I +  +Q + +P+DLE+LE  +ASIYY
Sbjct: 413 KLKEDAVSAFRLGYLSLTERAKAERLFWSCCHRIQEFLKQLDRIPEDLEDLERVMASIYY 472

Query: 506 ANMSVFQSAPDSWAIDQLFPIMPIHRLDEEPTQRGILADITCDSDGKIDQFIDLRDVKSV 565
            N+SVFQSAPD+WAIDQLFPIMPIHRL+EEP QR  LAD+TCDSDGKID+FIDL DVKS 
Sbjct: 473 VNLSVFQSAPDTWAIDQLFPIMPIHRLNEEPNQRVTLADLTCDSDGKIDRFIDLLDVKST 532

Query: 566 LELHPLIEVHQPGTPPRVEPYYLGMFLVGAYQEIMGNLHNLFGDINVVHIQMNPKGYQIE 625
           LELH L    QP      +PY LGMFL GAYQEIMGNLHNLFGD N VHI++ PKGY IE
Sbjct: 533 LELHSL----QPD-----QPYVLGMFLGGAYQEIMGNLHNLFGDTNAVHIKLTPKGYSIE 583

Query: 626 HLVRGDTIAEVLGYVQYDPEDLLENMRRYCEQAMEDKRMSLEEAQLLLENYERSLLQYTY 685
           H+V+GDT+ EVLGYVQYD E LLE +R+  E A++  ++SL+EAQ LL +YE  L +YTY
Sbjct: 584 HVVKGDTMGEVLGYVQYDTEQLLERLRQQTEAALQQDQISLDEAQRLLRHYEEGLQRYTY 643

Query: 686 L 686
           L
Sbjct: 644 L 644


Lambda     K      H
   0.319    0.137    0.402 

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: 1142
Number of extensions: 41
Number of successful extensions: 4
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: 695
Length of database: 647
Length adjustment: 39
Effective length of query: 656
Effective length of database: 608
Effective search space:   398848
Effective search space used:   398848
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)

Align candidate Synpcc7942_1037 Synpcc7942_1037 (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.27123.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-238  779.8   0.0   1.1e-238  779.6   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_1037  Synpcc7942_1037 arginine decarbo


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_1037  Synpcc7942_1037 arginine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  779.6   0.0  1.1e-238  1.1e-238       1     624 []      20     645 ..      20     645 .. 0.98

  Alignments for each domain:
  == domain 1  score: 779.6 bits;  conditional E-value: 1.1e-238
                                 TIGR01273   1 wsaeesakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrFpdilqk 69 
                                               w++e+s+++Y+i+gWg++yf +n++G+++v+p+g++   + dl+elv++++ +gl+lPll+rFpdil++
  lcl|FitnessBrowser__SynE:Synpcc7942_1037  20 WRIEDSEALYRIQGWGEPYFGINAAGHITVSPQGDR-GGSLDLYELVEALRRRGLNLPLLIRFPDILED 87 
                                               78999****************************998.99****************************** PP

                                 TIGR01273  70 rikslnaaFkeaieeleYaskyqavyPiKvnqqrevveelvasg.gkslGLEaGsKpEllialalaekp 137
                                               ri++lna F++ai +++Ya++y++v+P+K+nqqr+++e+lv+ g   ++GLEaGsKpElliala++++p
  lcl|FitnessBrowser__SynE:Synpcc7942_1037  88 RIERLNACFAKAIARYNYAGEYRGVFPVKCNQQRHLIESLVNYGrPFQFGLEAGSKPELLIALAHLDTP 156
                                               ********************************************99*********************** PP

                                 TIGR01273 138 kavivcnGyKDreyielaliarklglkvviviekleEldlvieeakklgvkPklGlRvrLaskgsgkwa 206
                                               +a+++cnGyKDr+yie+a+++r+lg   ++vie+leE+d+ i+ +++lg++P lG+R++L+++g g+w+
  lcl|FitnessBrowser__SynE:Synpcc7942_1037 157 GALLICNGYKDRDYIETAILGRRLGKTPILVIEQLEEVDVAIAASQRLGIEPILGVRAKLNARGMGRWG 225
                                               ********************************************************************* PP

                                 TIGR01273 207 ssgGeksKFGLsasqvlevvkklkeedlldslkllHfHlGsqianiddvkkgvrEaarlyvelrklGvk 275
                                               ss+G+++KFGL++ +++++v+kl++++ll++l+llHfH+Gsqi++i+ +k++++Eaa++yv+l  lG++
  lcl|FitnessBrowser__SynE:Synpcc7942_1037 226 SSAGDRAKFGLTMPEIVAAVEKLQAANLLHCLQLLHFHIGSQISDISVLKDAIQEAAQIYVQLAALGAD 294
                                               ********************************************************************* PP

                                 TIGR01273 276 ievvdvGGGLgvdYdGtksksdlsvnYsleeyaaavvaalkevceekgvpePviisEsGRaitahhavl 344
                                               ++++dvGGGLgvdYdG+k + + s nY+++ ya++vva++k++c+++ +  P++ sEsGRai++h +vl
  lcl|FitnessBrowser__SynE:Synpcc7942_1037 295 MRYLDVGGGLGVDYDGSKTNFHASKNYNMQTYANDVVATIKDACQAHRLAVPTLTSESGRAIASHQSVL 363
                                               ********************************************************************* PP

                                 TIGR01273 345 vaevleveeeeeeeaeeileeeapeevkeleellkeideesaeelledavqlleeavelfklGkldlee 413
                                               v++vl+ +e ++  +e   +ee +++v++l e+l++i  e+++e+++da++l+e+av++f+lG+l+l+e
  lcl|FitnessBrowser__SynE:Synpcc7942_1037 364 VFDVLGSSEVPRAAVEP-PQEEDSAIVRTLYEVLEAIALENLQECYHDAFKLKEDAVSAFRLGYLSLTE 431
                                               ********999996655.5559999******************************************** PP

                                 TIGR01273 414 ralaeqlalailkkvkeleakekshreildelqeklaekylvnlslFqslPDaWgidqlfPilPlerLd 482
                                               ra ae+l+ + +++++e+ ++   + e l++l+  +a+ y+vnls+Fqs PD+W+idqlfPi+P++rL+
  lcl|FitnessBrowser__SynE:Synpcc7942_1037 432 RAKAERLFWSCCHRIQEFLKQLDRIPEDLEDLERVMASIYYVNLSVFQSAPDTWAIDQLFPIMPIHRLN 500
                                               *****************77888888888999************************************** PP

                                 TIGR01273 483 ekpdrravllDltCDsDGkikkfveeqgiektlplheldkdeeyllgfflvGAYqEiLgdvHnLFgdte 551
                                               e+p++r +l+DltCDsDGki++f++  + ++tl lh+l++d++y+lg+fl GAYqEi+g+ HnLFgdt+
  lcl|FitnessBrowser__SynE:Synpcc7942_1037 501 EEPNQRVTLADLTCDSDGKIDRFIDLLDVKSTLELHSLQPDQPYVLGMFLGGAYQEIMGNLHNLFGDTN 569
                                               ********************************************************************* PP

                                 TIGR01273 552 avevvvkekgeveveaieegdtvedvlkavqydpeellkalkqk....vaeaklkaeekkqvlelleag 616
                                               av++ ++ kg +++e++++gdt+ +vl +vqyd+e+ll++l+q+     ++ +++ +e++++l  +e+g
  lcl|FitnessBrowser__SynE:Synpcc7942_1037 570 AVHIKLTPKG-YSIEHVVKGDTMGEVLGYVQYDTEQLLERLRQQteaaLQQDQISLDEAQRLLRHYEEG 637
                                               *********9.********************************988776777899************** PP

                                 TIGR01273 617 lsgypYLs 624
                                               l++y+YLs
  lcl|FitnessBrowser__SynE:Synpcc7942_1037 638 LQRYTYLS 645
                                               ******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (624 nodes)
Target sequences:                          1  (647 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 10.99
//
[ok]

This GapMind analysis is from Sep 17 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:

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:

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:

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, or view the source code.

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