Alignments for a candidate for putA in Calditerrivibrio nitroreducens DSM 19672

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Calditerrivibrio nitroreducens DSM 19672

Align delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized)
to candidate WP_013451009.1 CALNI_RS04425 1-pyrroline-5-carboxylate dehydrogenase

Query= CharProtDB::CH_122352
         (572 letters)



>NCBI__GCF_000183405.1:WP_013451009.1
          Length = 546

 Score =  506 bits (1304), Expect = e-148
 Identities = 264/542 (48%), Positives = 350/542 (64%), Gaps = 7/542 (1%)

Query: 28  ATYKVPRIDNEPNKHYAAGSPDRKALQEALARTQRNAPLSVPLVIAGKEVKSSSSLTQSN 87
           A   VP   NE    YA G+ +R  L+ AL +  ++  + +PL+I GKE+++        
Sbjct: 6   AIVNVPYPQNEAQYSYAPGTKERDLLKNAL-KDLKSQVIDIPLIIGGKEIRTGDKGKIVC 64

Query: 88  PASHGPV-ATYSNATAKDVQAAIESALEARKSWASTPFADRASVFLKAADLISTKYRYDV 146
           P +HG V A Y  A  K+V  AIE + +A K W    + +R S+FLKAADL+STKYRY +
Sbjct: 65  PHNHGHVLAEYHKAGEKEVLLAIEESQKAWKEWQKLRYEERISIFLKAADLLSTKYRYLL 124

Query: 147 MALTMHGQGKNAWQAEIDSAAELCDFFRFGVKYAEDLYAQQPVHHAPGVWNRVEYRPLEG 206
            A TM    KNA+QAEIDSA EL DF+RF   YA+ +Y +QP++   G WN  + RPLEG
Sbjct: 125 NAATMLSISKNAYQAEIDSACELIDFWRFNSYYAQQIYKEQPLYSPKGTWNYTQQRPLEG 184

Query: 207 FVYAISPFNFTAIGGNLAGAPALMGNVVVWKPSPSAIASNWLVHQILLEAGLPKNVIQFV 266
           F++A++PFNFTAIGGNL  +PA+MGNVV+WKP+ SAI + + + +IL EAGLP  VI F+
Sbjct: 185 FIFAVTPFNFTAIGGNLPTSPAIMGNVVLWKPASSAIYAPYFIMKILQEAGLPDGVINFI 244

Query: 267 PGEAEEVTKTVLDHPDFAALHFTGSTNVFRNLYGQISTRVAAGKYRSYPRIVGETGGKNF 326
           PG A  V    + HP  A +HFTGST VF+ ++  +   +A  KY +YPRIVGETGGK+F
Sbjct: 245 PGSASIVGDICIKHPLMAGIHFTGSTAVFQKMWKDVGANIA--KYTNYPRIVGETGGKDF 302

Query: 327 HLIHKSADIRNAAVQTVRGAFEYQGQKCSATSRVYVASSIADSFLEQVASEAKSLKVGPP 386
              H SADI+   V  VRGAFEYQGQKCSA SR Y+  SI     E + +E K+LK+G  
Sbjct: 303 VFAHSSADIKKLVVALVRGAFEYQGQKCSAASRAYIPRSIWGKTWEIMEAELKNLKMGDV 362

Query: 387 SDFTNFCGPVIHEASFTKLAKVIDEAKNDPELELLAGGSYDSSKGWYIQPTVYRTTNPDH 446
            DFTN    VI E++F  + + ID AKN  + E++ GG YD S G++I+PTV    +P  
Sbjct: 363 EDFTNLINAVIDESAFESITEYIDYAKNSKDAEIIFGGKYDKSIGYFIEPTVILAKDPHF 422

Query: 447 PLLTRELFGPILVVYAYPDATEADFARIAQKIDATGEYGLTGSVFAQDREALAVANDVLR 506
             +  E+FGP+L +Y Y D     F    +  D T  Y LTG++FA DR+ +++  + L 
Sbjct: 423 KTMEEEIFGPVLTIYVYDD---EKFEETLEICDRTSPYALTGAIFANDRKVISMMMEKLE 479

Query: 507 NAAGNFYINCKSTGAVVGQQPFGGARASGTNDKAGSGNLLSRFVSLRSIKEEFVPTYKVA 566
            AAGNFYIN K TGAVVGQQPFGG RASGTNDKAGS   L R+VS R++KE F+   ++ 
Sbjct: 480 FAAGNFYINDKPTGAVVGQQPFGGGRASGTNDKAGSILNLYRWVSTRAVKENFIAPDEIG 539

Query: 567 YP 568
           YP
Sbjct: 540 YP 541


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: 846
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: 546
Length adjustment: 36
Effective length of query: 536
Effective length of database: 510
Effective search space:   273360
Effective search space used:   273360
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_013451009.1 CALNI_RS04425 (1-pyrroline-5-carboxylate 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.17170.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     4e-242  790.4   0.2   4.6e-242  790.2   0.2    1.0  1  lcl|NCBI__GCF_000183405.1:WP_013451009.1  CALNI_RS04425 1-pyrroline-5-carb


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000183405.1:WP_013451009.1  CALNI_RS04425 1-pyrroline-5-carboxylate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  790.2   0.2  4.6e-242  4.6e-242       2     532 ..      15     543 ..      14     544 .. 0.99

  Alignments for each domain:
  == domain 1  score: 790.2 bits;  conditional E-value: 4.6e-242
                                 TIGR01236   2 nePvkefrpgskerdllrkelkelkskvleiPlviggkevvksnelievvaPadhqaklakltnateed 70 
                                               ne   +++pg+kerdll+++lk+lks+v++iPl+iggke+ + + + ++v P++h ++la+ ++a+e++
  lcl|NCBI__GCF_000183405.1:WP_013451009.1  15 NEAQYSYAPGTKERDLLKNALKDLKSQVIDIPLIIGGKEIRTGD-KGKIVCPHNHGHVLAEYHKAGEKE 82 
                                               899999*********************************66655.79********************** PP

                                 TIGR01236  71 vkkaveaaldakkeWselpfadraaiflkaadllsgkyreeilaatmlgqsktvyqaeidavaelidff 139
                                               v  a+e + +a+keW++l +++r +iflkaadlls+kyr+ ++aatml+ sk+ yqaeid+++elidf+
  lcl|NCBI__GCF_000183405.1:WP_013451009.1  83 VLLAIEESQKAWKEWQKLRYEERISIFLKAADLLSTKYRYLLNAATMLSISKNAYQAEIDSACELIDFW 151
                                               ********************************************************************* PP

                                 TIGR01236 140 rfnvkyarelleqqPsvsapgelnkveyrpleGfvaaisPfnftaiaanlagaPalmGnvvvWkPskta 208
                                               rfn +ya+++++ qP  s +g++n ++ rpleGf++a++Pfnftai++nl+++Pa+mGnvv+WkP++ a
  lcl|NCBI__GCF_000183405.1:WP_013451009.1 152 RFNSYYAQQIYKEQPLYSPKGTWNYTQQRPLEGFIFAVTPFNFTAIGGNLPTSPAIMGNVVLWKPASSA 220
                                               ****************9**************************************************** PP

                                 TIGR01236 209 vlsnyllmkileeaGlPpgvinfvpadgvkvsdvvladkdlaalhftGstavfkelwkkvasnldkyrn 277
                                               +++ y +mkil+eaGlP gvinf+p+ +  v+d+   ++ +a++hftGstavf+++wk v  n+ ky n
  lcl|NCBI__GCF_000183405.1:WP_013451009.1 221 IYAPYFIMKILQEAGLPDGVINFIPGSASIVGDICIKHPLMAGIHFTGSTAVFQKMWKDVGANIAKYTN 289
                                               ********************************************************************* PP

                                 TIGR01236 278 fPrivGetGGkdfvlvhpsadveevvaatirgafeyqGqkcsaasrlyvpkslwkelkeellaelkkvk 346
                                               +PrivGetGGkdfv++h+sad++++v+a++rgafeyqGqkcsaasr+y+p+s+w + +e + aelk++k
  lcl|NCBI__GCF_000183405.1:WP_013451009.1 290 YPRIVGETGGKDFVFAHSSADIKKLVVALVRGAFEYQGQKCSAASRAYIPRSIWGKTWEIMEAELKNLK 358
                                               ********************************************************************* PP

                                 TIGR01236 347 vgdvddlssfmgavideksfakivkviekakkdpeeleilaGGkyddskGyfvePtvveskdPkeklmk 415
                                               +gdv+d+++ + avide +f+ i ++i++ak++  + ei+ GGkyd+s Gyf+ePtv+++kdP+ k+m+
  lcl|NCBI__GCF_000183405.1:WP_013451009.1 359 MGDVEDFTNLINAVIDESAFESITEYIDYAKNSK-DAEIIFGGKYDKSIGYFIEPTVILAKDPHFKTME 426
                                               *******************************955.9********************************* PP

                                 TIGR01236 416 eeifGPvltvyvydddkykeilevvdstskyaltGavfakdreaieeaekklrfaaGnfyindkstGav 484
                                               eeifGPvlt+yvydd+k++e+le+ d+ts yaltGa+fa+dr++i    +kl faaGnfyindk+tGav
  lcl|NCBI__GCF_000183405.1:WP_013451009.1 427 EEIFGPVLTIYVYDDEKFEETLEICDRTSPYALTGAIFANDRKVISMMMEKLEFAAGNFYINDKPTGAV 495
                                               ********************************************************************* PP

                                 TIGR01236 485 vgqqpfGGarlsGtndkaGapkillrfvsarsiketfkeltdfkypym 532
                                               vgqqpfGG r+sGtndkaG+  +l r+vs+r++ke+f ++ ++ yp+m
  lcl|NCBI__GCF_000183405.1:WP_013451009.1 496 VGQQPFGGGRASGTNDKAGSILNLYRWVSTRAVKENFIAPDEIGYPFM 543
                                               **********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (533 nodes)
Target sequences:                          1  (546 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: 00:00:00.02
# Mc/sec: 12.20
//
[ok]

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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