Alignments for a candidate for aspA in Photobacterium gaetbulicola Gung47

GapMind for catabolism of small carbon sources

Alignments for a candidate for aspA in Photobacterium gaetbulicola Gung47

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate WP_044622067.1 H744_RS09165 aspartate ammonia-lyase

Query= BRENDA::P0AC38
         (478 letters)



>NCBI__GCF_000940995.1:WP_044622067.1
          Length = 487

 Score =  763 bits (1969), Expect = 0.0
 Identities = 376/474 (79%), Positives = 418/474 (88%), Gaps = 2/474 (0%)

Query: 1   MSNNI--RIEEDLLGTREVPADAYYGVHTLRAIENFYISNNKISDIPEFVRGMVMVKKAA 58
           M+NN+  RIEEDLLG R+VPADAY+G+HTLRA+ENF ISN  ISD+PEFVRGMV  KKAA
Sbjct: 13  MANNVATRIEEDLLGERQVPADAYWGIHTLRAVENFNISNTTISDVPEFVRGMVFTKKAA 72

Query: 59  AMANKELQTIPKSVANAIIAACDEVLNNGKCMDQFPVDVYQGGAGTSVNMNTNEVLANIG 118
           AMANKEL  IP  V   II ACD +L  GKCMDQFP DVYQGGAGTSVNMNTNEV+AN+ 
Sbjct: 73  AMANKELGVIPSEVGEYIIKACDVILETGKCMDQFPSDVYQGGAGTSVNMNTNEVIANLA 132

Query: 119 LELMGHQKGEYQYLNPNDHVNKCQSTNDAYPTGFRIAVYSSLIKLVDAINQLREGFERKA 178
           LELMG +KGEY  +NPNDHVNK QSTN AYPTGFR+AVY+S++ +++A+  L+  F+ K 
Sbjct: 133 LELMGKEKGEYDIVNPNDHVNKSQSTNCAYPTGFRVAVYNSIMTMLEALEYLKGAFDAKD 192

Query: 179 VEFQDILKMGRTQLQDAVPMTLGQEFRAFSILLKEEVKNIQRTAELLLEVNLGATAIGTG 238
            EF ++LKMGRTQLQDAVPMT+GQEF AF +L+KEE+KN+Q TA+LLLEVNLGATAIGTG
Sbjct: 193 KEFANVLKMGRTQLQDAVPMTVGQEFHAFGVLIKEEIKNLQYTAQLLLEVNLGATAIGTG 252

Query: 239 LNTPKEYSPLAVKKLAEVTGFPCVPAEDLIEATSDCGAYVMVHGALKRLAVKMSKICNDL 298
           LN    Y  LAV++LAEVTG PCVPAEDLIEATSDCGAYVMVHGALKR AVK+SKICNDL
Sbjct: 253 LNAATGYQELAVQRLAEVTGLPCVPAEDLIEATSDCGAYVMVHGALKRTAVKLSKICNDL 312

Query: 299 RLLSSGPRAGLNEINLPELQAGSSIMPAKVNPVVPEVVNQVCFKVIGNDTTVTMAAEAGQ 358
           RLLSSGPRAGLNEINLPE+QAGSSIMPAKVNPVVPEVVNQVCFKVIGNDTT+T AAEAGQ
Sbjct: 313 RLLSSGPRAGLNEINLPEMQAGSSIMPAKVNPVVPEVVNQVCFKVIGNDTTITFAAEAGQ 372

Query: 359 LQLNVMEPVIGQAMFESVHILTNACYNLLEKCINGITANKEVCEGYVYNSIGIVTYLNPF 418
           LQLNVMEPVIGQA+FES+ IL NAC NL +KCI+GIT NKEVCE +V+NSIGIVTYLNPF
Sbjct: 373 LQLNVMEPVIGQALFESIDILKNACINLRDKCIDGITVNKEVCESFVFNSIGIVTYLNPF 432

Query: 419 IGHHNGDIVGKICAETGKSVREVVLERGLLTEAELDDIFSVQNLMHPAYKAKRY 472
           IGHH GDIVGKICAETGKSVREVVLERGLLTE +LDDIFSVQNLMHP YKAKRY
Sbjct: 433 IGHHEGDIVGKICAETGKSVREVVLERGLLTEEQLDDIFSVQNLMHPEYKAKRY 486


Lambda     K      H
   0.317    0.134    0.381 

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: 746
Number of extensions: 23
Number of successful extensions: 1
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: 478
Length of database: 487
Length adjustment: 34
Effective length of query: 444
Effective length of database: 453
Effective search space:   201132
Effective search space used:   201132
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: 52 (24.6 bits)

Align candidate WP_044622067.1 H744_RS09165 (aspartate ammonia-lyase)
to HMM TIGR00839 (aspA: aspartate ammonia-lyase (EC 4.3.1.1))

# 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/TIGR00839.hmm
# target sequence database:        /tmp/gapView.333125.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00839  [M=468]
Accession:   TIGR00839
Description: aspA: aspartate ammonia-lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.9e-261  852.4   4.3   5.6e-261  852.2   4.3    1.0  1  NCBI__GCF_000940995.1:WP_044622067.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000940995.1:WP_044622067.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  852.2   4.3  5.6e-261  5.6e-261       1     466 [.      20     486 ..      20     487 .] 1.00

  Alignments for each domain:
  == domain 1  score: 852.2 bits;  conditional E-value: 5.6e-261
                             TIGR00839   1 riekdllGekeveaevyyGiqtlrasenfaisnekisdvpefvkalvlvkkaaalanvelkaidekiakaiva 73 
                                           rie+dllGe++v+a++y+Gi+tlra+enf+isn++isdvpefv+++v  kkaaa+an+el+ i++++++ i++
  NCBI__GCF_000940995.1:WP_044622067.1  20 RIEEDLLGERQVPADAYWGIHTLRAVENFNISNTTISDVPEFVRGMVFTKKAAAMANKELGVIPSEVGEYIIK 92 
                                           89*********************************************************************** PP

                             TIGR00839  74 acdeile.GkyldqfivdviqGGaGtsvnmntnevianlalellGhkkGeyqflnpndhvnksqstndaypta 145
                                           acd ile Gk++dqf++dv+qGGaGtsvnmntnevianlalel+G++kGey  +npndhvnksqstn aypt+
  NCBI__GCF_000940995.1:WP_044622067.1  93 ACDVILEtGKCMDQFPSDVYQGGAGTSVNMNTNEVIANLALELMGKEKGEYDIVNPNDHVNKSQSTNCAYPTG 165
                                           ************************************************************************* PP

                             TIGR00839 146 lkiavyesleklvdkiealrdafeqkakefadvlkmGrtqlqdavpltlGqefeayalllerdvkrikrtrel 218
                                           +++avy+s++ +++++e+l+ af+ k kefa+vlkmGrtqlqdavp+t+Gqef+a+ +l+++++k+++ t++l
  NCBI__GCF_000940995.1:WP_044622067.1 166 FRVAVYNSIMTMLEALEYLKGAFDAKDKEFANVLKMGRTQLQDAVPMTVGQEFHAFGVLIKEEIKNLQYTAQL 238
                                           ************************************************************************* PP

                             TIGR00839 219 llevnlGataiGtGlnadkeysklvvkklaevtGlplvpaenlieatsdtgayvevsgalkriavklskvcnd 291
                                           llevnlGataiGtGlna  +y++l+v++laevtGlp+vpae+lieatsd+gayv+v+galkr+avklsk+cnd
  NCBI__GCF_000940995.1:WP_044622067.1 239 LLEVNLGATAIGTGLNAATGYQELAVQRLAEVTGLPCVPAEDLIEATSDCGAYVMVHGALKRTAVKLSKICND 311
                                           ************************************************************************* PP

                             TIGR00839 292 lrllssGpraGlneinlpelqaGssimpakvnpvvpevvnqvcfkviGndttvtlaaeaGqlqlnvlepviaf 364
                                           lrllssGpraGlneinlpe+qaGssimpakvnpvvpevvnqvcfkviGndtt+t+aaeaGqlqlnv+epvi++
  NCBI__GCF_000940995.1:WP_044622067.1 312 LRLLSSGPRAGLNEINLPEMQAGSSIMPAKVNPVVPEVVNQVCFKVIGNDTTITFAAEAGQLQLNVMEPVIGQ 384
                                           ************************************************************************* PP

                             TIGR00839 365 allesisiltnaiesltdkcveGitanekicedyvfnsiGivtalnpfiGyekaalvakeaiktgksvrdvvl 437
                                           al+esi+il+na+ +l+dkc++Git+n+++ce++vfnsiGivt+lnpfiG++++++v+k++++tgksvr+vvl
  NCBI__GCF_000940995.1:WP_044622067.1 385 ALFESIDILKNACINLRDKCIDGITVNKEVCESFVFNSIGIVTYLNPFIGHHEGDIVGKICAETGKSVREVVL 457
                                           ************************************************************************* PP

                             TIGR00839 438 ekdllteeelddilsvenllkpaykakkl 466
                                           e++lltee+lddi+sv+nl++p ykak++
  NCBI__GCF_000940995.1:WP_044622067.1 458 ERGLLTEEQLDDIFSVQNLMHPEYKAKRY 486
                                           ***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (468 nodes)
Target sequences:                          1  (487 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 28.66
//
[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 2024 update 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