Alignments for a candidate for putA in Mycolicibacterium vanbaalenii PYR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Mycolicibacterium vanbaalenii PYR-1

Align Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; P5C dehydrogenase; Aldehyde dehydrogenase family 4 member A1; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_011781678.1 MVAN_RS22735 1-pyrroline-5-carboxylate dehydrogenase

Query= SwissProt::Q8CHT0
         (562 letters)



>NCBI__GCF_000015305.1:WP_011781678.1
          Length = 542

 Score =  485 bits (1249), Expect = e-141
 Identities = 248/532 (46%), Positives = 338/532 (63%), Gaps = 2/532 (0%)

Query: 32  TNEPILAFSQGSPERDALQKALKDLKGQMEAIPCVVGDEEVWTSDIQYQL-SPFNHAHKV 90
           +NEP+  ++ GSPER  L+  L DL      +P V+G      +    ++  P  H+ ++
Sbjct: 11  SNEPVHEYAPGSPERHRLENMLADLAADPIELPHVIGGTHRMGAGPSVEVVQPHRHSARL 70

Query: 91  AKFCYADKALLNRAIDAALAARKEWDLKPMADRAQVFLKAADMLSGPRRAEVLAKTMVGQ 150
                AD A    A++AA+AA+  W+  P  +RA VFL+AAD+++GP R ++ A TM+GQ
Sbjct: 71  GICTNADHADAAAAVEAAVAAKPGWENTPFDERAAVFLRAADLMAGPWREKIAAATMLGQ 130

Query: 151 GKTVIQAEIDAAAELIDFFRFNAKFAVELEGEQPISVPPSTNHTVYRGLEGFVAAISPFN 210
            KT  QAEIDA  EL+DF+RFN  FA ++  +QP++     N T YR LEGFV AI+PFN
Sbjct: 131 SKTAYQAEIDAPCELVDFWRFNVAFARQILAQQPLNSKGVWNRTDYRPLEGFVYAITPFN 190

Query: 211 FTAIGGNLAGAPALMGNVVLWKPSDTAMLASYAVYRILREAGLPPNIIQFVPADGPTFGD 270
           FTAI GNL  APALMGN V+WKPS T M A+Y   ++L  AGLPP +I  +  DG    D
Sbjct: 191 FTAIAGNLPTAPALMGNTVVWKPSPTQMFAAYLTMQLLEAAGLPPGVINLLAGDGLAVSD 250

Query: 271 TVTSSEHLCGINFTGSVPTFKHLWRQVAQNLDRFRTFPRLAGECGGKNFHFVHSSADVDS 330
            + S   L GI+FTGS  TF+HLWR+V  ++DR+ T+PRL GE GGK+F   H SA  D 
Sbjct: 251 VLLSDRRLAGIHFTGSTATFQHLWREVGTHIDRYDTYPRLVGETGGKDFVVAHPSAQPDV 310

Query: 331 VVSGTLRSAFEYGGQKCSACSRLYVPKSLWPQIKGRLLEEHSRIKVGDPAEDFGTFFSAV 390
           + +  +R AF+Y GQKCSA SR Y+ +S+W ++    L+    +  GD  E    F  A+
Sbjct: 311 LRTALIRGAFDYQGQKCSAASRAYIARSVWQKMGDDFLDTTEALPYGDVTE-LANFGGAL 369

Query: 391 IDAKAFARIKKWLEHARSSPSLSILAGGQCNESVGYYVEPCIIESKDPQEPIMKEEIFGP 450
           ID +AF +    +E A+S+  ++I  GG+ ++S GY+V P ++ S DP +     E FGP
Sbjct: 370 IDERAFVKNVTAIERAKSAAGVTIAVGGEYDDSEGYFVRPTVLLSDDPGDEAFSTEYFGP 429

Query: 451 VLTVYVYPDDKYRETLQLVDSTTSYGLTGAVFAQDKAIVQEATRMLRNAAGNFYINDKST 510
           +L V+VYPD+ Y   L +VD++  Y LTGAV A D+A V  A R LR+AAGNFY+NDK T
Sbjct: 430 LLAVHVYPDEDYERILDVVDTSARYALTGAVIADDRAAVLTAERRLRHAAGNFYVNDKPT 489

Query: 511 GSVVGQQPFGGARASGTNDKPGGPHYILRWTSPQVIKETHKPLGDWRYSYMQ 562
           G+VVGQQPFGG+RASGTNDK G    +LRWTS + IKET  P     Y +M+
Sbjct: 490 GAVVGQQPFGGSRASGTNDKAGSALNLLRWTSARSIKETFVPPTSHTYPHME 541


Lambda     K      H
   0.319    0.135    0.411 

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: 843
Number of extensions: 42
Number of successful extensions: 3
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: 562
Length of database: 542
Length adjustment: 36
Effective length of query: 526
Effective length of database: 506
Effective search space:   266156
Effective search space used:   266156
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: 53 (25.0 bits)

Align candidate WP_011781678.1 MVAN_RS22735 (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.24846.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-259  848.4   0.0   1.2e-259  848.2   0.0    1.0  1  lcl|NCBI__GCF_000015305.1:WP_011781678.1  MVAN_RS22735 1-pyrroline-5-carbo


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011781678.1  MVAN_RS22735 1-pyrroline-5-carboxylate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  848.2   0.0  1.2e-259  1.2e-259       2     532 ..      12     540 ..      11     541 .. 0.99

  Alignments for each domain:
  == domain 1  score: 848.2 bits;  conditional E-value: 1.2e-259
                                 TIGR01236   2 nePvkefrpgskerdllrkelkelkskvleiPlviggkevvksnelievvaPadhqaklakltnateed 70 
                                               nePv+e++pgs+er++l++ l++l+ + +e+P+vigg +++  +  +evv+P++h+a+l+  tna+++d
  lcl|NCBI__GCF_000015305.1:WP_011781678.1  12 NEPVHEYAPGSPERHRLENMLADLAADPIELPHVIGGTHRMGAGPSVEVVQPHRHSARLGICTNADHAD 80 
                                               9******************************************************************** PP

                                 TIGR01236  71 vkkaveaaldakkeWselpfadraaiflkaadllsgkyreeilaatmlgqsktvyqaeidavaelidff 139
                                               +++aveaa++ak  W++ pf++raa+fl+aadl++g++re+i+aatmlgqskt yqaeida +el+df+
  lcl|NCBI__GCF_000015305.1:WP_011781678.1  81 AAAAVEAAVAAKPGWENTPFDERAAVFLRAADLMAGPWREKIAAATMLGQSKTAYQAEIDAPCELVDFW 149
                                               ********************************************************************* PP

                                 TIGR01236 140 rfnvkyarelleqqPsvsapgelnkveyrpleGfvaaisPfnftaiaanlagaPalmGnvvvWkPskta 208
                                               rfnv++ar++l+qqP  +++g++n+++yrpleGfv+ai+Pfnftaia+nl++aPalmGn+vvWkPs t+
  lcl|NCBI__GCF_000015305.1:WP_011781678.1 150 RFNVAFARQILAQQP-LNSKGVWNRTDYRPLEGFVYAITPFNFTAIAGNLPTAPALMGNTVVWKPSPTQ 217
                                               ***************.799************************************************** PP

                                 TIGR01236 209 vlsnyllmkileeaGlPpgvinfvpadgvkvsdvvladkdlaalhftGstavfkelwkkvasnldkyrn 277
                                               ++++yl+m++le+aGlPpgvin++++dg +vsdv l+d++la++hftGsta+f++lw++v +++d+y +
  lcl|NCBI__GCF_000015305.1:WP_011781678.1 218 MFAAYLTMQLLEAAGLPPGVINLLAGDGLAVSDVLLSDRRLAGIHFTGSTATFQHLWREVGTHIDRYDT 286
                                               ********************************************************************* PP

                                 TIGR01236 278 fPrivGetGGkdfvlvhpsadveevvaatirgafeyqGqkcsaasrlyvpkslwkelkeellaelkkvk 346
                                               +Pr+vGetGGkdfv++hpsa+ +++++a+irgaf+yqGqkcsaasr+y+++s+w+++ +++l++++ + 
  lcl|NCBI__GCF_000015305.1:WP_011781678.1 287 YPRLVGETGGKDFVVAHPSAQPDVLRTALIRGAFDYQGQKCSAASRAYIARSVWQKMGDDFLDTTEALP 355
                                               ********************************************************************* PP

                                 TIGR01236 347 vgdvddlssfmgavideksfakivkviekakkdpeeleilaGGkyddskGyfvePtvveskdPkeklmk 415
                                               +gdv++l +f ga+ide++f k+v +ie+ak+ +  ++i++GG+ydds+Gyfv+Ptv++s+dP ++ ++
  lcl|NCBI__GCF_000015305.1:WP_011781678.1 356 YGDVTELANFGGALIDERAFVKNVTAIERAKSAA-GVTIAVGGEYDDSEGYFVRPTVLLSDDPGDEAFS 423
                                               *******************************955.********************************** PP

                                 TIGR01236 416 eeifGPvltvyvydddkykeilevvdstskyaltGavfakdreaieeaekklrfaaGnfyindkstGav 484
                                               +e+fGP+l+v+vy+d+ y+ il+vvd++++yaltGav+a+dr+a+++ae +lr+aaGnfy+ndk+tGav
  lcl|NCBI__GCF_000015305.1:WP_011781678.1 424 TEYFGPLLAVHVYPDEDYERILDVVDTSARYALTGAVIADDRAAVLTAERRLRHAAGNFYVNDKPTGAV 492
                                               ********************************************************************* PP

                                 TIGR01236 485 vgqqpfGGarlsGtndkaGapkillrfvsarsiketfkeltdfkypym 532
                                               vgqqpfGG+r+sGtndkaG++ +llr++sarsiketf+++t ++yp+m
  lcl|NCBI__GCF_000015305.1:WP_011781678.1 493 VGQQPFGGSRASGTNDKAGSALNLLRWTSARSIKETFVPPTSHTYPHM 540
                                               ***********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (533 nodes)
Target sequences:                          1  (542 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: 10.57
//
[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