GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Dyadobacter tibetensis Y620-1

Align delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized)
to candidate WP_025765157.1 X939_RS0120545 L-glutamate gamma-semialdehyde dehydrogenase

Query= CharProtDB::CH_122352
         (572 letters)



>NCBI__GCF_000566685.1:WP_025765157.1
          Length = 543

 Score =  508 bits (1308), Expect = e-148
 Identities = 272/540 (50%), Positives = 349/540 (64%), Gaps = 8/540 (1%)

Query: 30  YKVPRIDNEPNKHYAAGSPDRKALQEALARTQRNAPLSVPLVIAGKEVKSSSSLTQSNPA 89
           + VP + NEP K YA G+ +R  L+E L +  R   + +P  I G E  S   +  + P 
Sbjct: 6   FLVPALKNEPIKSYAPGTAERAELKEMLDQA-RKVQIEIPQYIGGGEKYSGKKVRLAPPH 64

Query: 90  SHGPVATYSN-ATAKDVQAAIESALEARKSWASTPFADRASVFLKAADLISTKYRYDVMA 148
            H  V  Y +  TA DV+ AI  ALEAR  WA+  +  RA++FLKAADLI+  YR ++ A
Sbjct: 65  DHQHVLGYFHEGTAADVKLAITEALEARTKWAAMDWEQRAAIFLKAADLIAGPYRAEINA 124

Query: 149 LTMHGQGKNAWQAEIDSAAELCDFFRFGVKYAEDLYAQQPVHHAPGVWNRVEYRPLEGFV 208
            TM GQ KNA+QAEIDSA EL DF R  V + +++Y QQP+  + G+WNR+EYRPLEGFV
Sbjct: 125 ATMLGQSKNAYQAEIDSACELIDFLRMNVNFMQEIYEQQPIS-SDGIWNRMEYRPLEGFV 183

Query: 209 YAISPFNFTAIGGNLAGAPALMGNVVVWKPSPSAIASNWLVHQILLEAGLPKNVIQFVPG 268
           +AI+PFNFTAI GNL  APALMGNV +WKP+ + + +  ++ ++  EAGLP  VI  +  
Sbjct: 184 FAITPFNFTAIAGNLPAAPALMGNVTLWKPAFTQVYAANVIMKVFKEAGLPDGVINMILV 243

Query: 269 EAEEVTKTVLDHPDFAALHFTGSTNVFRNLYGQISTRVAAGKYRSYPRIVGETGGKNFHL 328
           +  E  + V  HPDFA +HFTGST VF+ ++  I   +A   Y+++PRIVGETGGK+F L
Sbjct: 244 DGPEAGEVVFKHPDFAGIHFTGSTKVFQTIWKTIGENIAG--YKTFPRIVGETGGKDFVL 301

Query: 329 IHKSADIRNAAVQTVRGAFEYQGQKCSATSRVYVASSIADSFLEQVASEAKSLKVGPPSD 388
            HKSA+ +  A   VRGAFEYQGQKCSA SR Y+ S+I +   E + ++   +K+G   D
Sbjct: 302 AHKSANAKALATGLVRGAFEYQGQKCSAASRAYIPSNIWEEVKEYIHADLAEIKMGGVED 361

Query: 389 FTNFCGPVIHEASFTKLAKVIDEAKNDPELELLAGGSYDSSKGWYIQPTVYRTTNPDHPL 448
           F NF   VI E +F K+   ID AK   E E++AGG+YD S G++I PTV    +PD+  
Sbjct: 362 FGNFINAVIDEKAFDKIVGYIDAAKASQEAEIIAGGTYDKSVGYFIAPTVILAHSPDYVT 421

Query: 449 LTRELFGPILVVYAYPDATEADFARIAQKIDATGEYGLTGSVFAQDREALAVANDVLRNA 508
           L  E+FGP+L +Y Y    E  F    Q +D T  Y LTG+VFA DR A+  A   L NA
Sbjct: 422 LCEEIFGPVLTIYVY---DENKFEETVQLVDQTSPYALTGAVFATDRYAIEYATTNLVNA 478

Query: 509 AGNFYINCKSTGAVVGQQPFGGARASGTNDKAGSGNLLSRFVSLRSIKEEFVPTYKVAYP 568
           AGNFYIN K TGAVVGQQPFGGARASGTNDKAGS   L R+VS R IKE FV      YP
Sbjct: 479 AGNFYINDKPTGAVVGQQPFGGARASGTNDKAGSILNLLRWVSPRVIKETFVSPISYQYP 538


Lambda     K      H
   0.316    0.130    0.379 

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: 865
Number of extensions: 40
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: 572
Length of database: 543
Length adjustment: 36
Effective length of query: 536
Effective length of database: 507
Effective search space:   271752
Effective search space used:   271752
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 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate WP_025765157.1 X939_RS0120545 (L-glutamate gamma-semialdehyde dehydrogenase)
to HMM TIGR01236 (pruA: 1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

# 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/TIGR01236.hmm
# target sequence database:        /tmp/gapView.3029401.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01236  [M=533]
Accession:   TIGR01236
Description: D1pyr5carbox1: 1-pyrroline-5-carboxylate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-241  787.9   1.6   2.7e-241  787.7   1.6    1.0  1  NCBI__GCF_000566685.1:WP_025765157.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000566685.1:WP_025765157.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  787.7   1.6  2.7e-241  2.7e-241       1     531 [.      12     539 ..      12     541 .. 0.99

  Alignments for each domain:
  == domain 1  score: 787.7 bits;  conditional E-value: 2.7e-241
                             TIGR01236   1 knePvkefrpgskerdllrkelkelkskvleiPlviggkevvksnelievvaPadhqaklakltnateedvkk 73 
                                           kneP+k+++pg+ er  l++ l ++++ ++eiP  igg e ++ + +++   P+dhq++l+ +++ t +dvk 
  NCBI__GCF_000566685.1:WP_025765157.1  12 KNEPIKSYAPGTAERAELKEMLDQARKVQIEIPQYIGGGEKYSGK-KVRLAPPHDHQHVLGYFHEGTAADVKL 83 
                                           6*************************************9977766.69************************* PP

                             TIGR01236  74 aveaaldakkeWselpfadraaiflkaadllsgkyreeilaatmlgqsktvyqaeidavaelidffrfnvkya 146
                                           a+  al+a+++W+++++++raaiflkaadl++g+yr+ei+aatmlgqsk+ yqaeid+++elidf+r nv++ 
  NCBI__GCF_000566685.1:WP_025765157.1  84 AITEALEARTKWAAMDWEQRAAIFLKAADLIAGPYRAEINAATMLGQSKNAYQAEIDSACELIDFLRMNVNFM 156
                                           ************************************************************************* PP

                             TIGR01236 147 relleqqPsvsapgelnkveyrpleGfvaaisPfnftaiaanlagaPalmGnvvvWkPsktavlsnyllmkil 219
                                           +e++eqqP +s++g +n++eyrpleGfv+ai+Pfnftaia+nl++aPalmGnv++WkP+ t+v+++ ++mk++
  NCBI__GCF_000566685.1:WP_025765157.1 157 QEIYEQQP-ISSDGIWNRMEYRPLEGFVFAITPFNFTAIAGNLPAAPALMGNVTLWKPAFTQVYAANVIMKVF 228
                                           ********.8*************************************************************** PP

                             TIGR01236 220 eeaGlPpgvinfvpadgvkvsdvvladkdlaalhftGstavfkelwkkvasnldkyrnfPrivGetGGkdfvl 292
                                           +eaGlP gvin++ +dg + ++vv  ++d+a++hftGst+vf+++wk++ +n+  y++fPrivGetGGkdfvl
  NCBI__GCF_000566685.1:WP_025765157.1 229 KEAGLPDGVINMILVDGPEAGEVVFKHPDFAGIHFTGSTKVFQTIWKTIGENIAGYKTFPRIVGETGGKDFVL 301
                                           ************************************************************************* PP

                             TIGR01236 293 vhpsadveevvaatirgafeyqGqkcsaasrlyvpkslwkelkeellaelkkvkvgdvddlssfmgavideks 365
                                           +h+sa+ + ++++++rgafeyqGqkcsaasr+y+p  +w+e+ke + a+l+++k+g v+d+ +f+ avidek+
  NCBI__GCF_000566685.1:WP_025765157.1 302 AHKSANAKALATGLVRGAFEYQGQKCSAASRAYIPSNIWEEVKEYIHADLAEIKMGGVEDFGNFINAVIDEKA 374
                                           ************************************************************************* PP

                             TIGR01236 366 fakivkviekakkdpeeleilaGGkyddskGyfvePtvveskdPkeklmkeeifGPvltvyvydddkykeile 438
                                           f+kiv +i+ ak++  e ei+aGG yd+s Gyf+ Ptv++++ P+  ++ eeifGPvlt+yvyd++k++e+++
  NCBI__GCF_000566685.1:WP_025765157.1 375 FDKIVGYIDAAKASQ-EAEIIAGGTYDKSVGYFIAPTVILAHSPDYVTLCEEIFGPVLTIYVYDENKFEETVQ 446
                                           *************65.********************************************************* PP

                             TIGR01236 439 vvdstskyaltGavfakdreaieeaekklrfaaGnfyindkstGavvgqqpfGGarlsGtndkaGapkillrf 511
                                           +vd+ts yaltGavfa dr aie+a+ +l +aaGnfyindk+tGavvgqqpfGGar+sGtndkaG+  +llr+
  NCBI__GCF_000566685.1:WP_025765157.1 447 LVDQTSPYALTGAVFATDRYAIEYATTNLVNAAGNFYINDKPTGAVVGQQPFGGARASGTNDKAGSILNLLRW 519
                                           ************************************************************************* PP

                             TIGR01236 512 vsarsiketfkeltdfkypy 531
                                           vs+r+iketf+++  ++yp+
  NCBI__GCF_000566685.1:WP_025765157.1 520 VSPRVIKETFVSPISYQYPF 539
                                           ******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (533 nodes)
Target sequences:                          1  (543 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 16.18
//
[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:

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:

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