Alignments for a candidate for aspA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for aspA in Pseudomonas simiae WCS417

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate GFF5496 PS417_28130 aspartate ammonia-lyase

Query= BRENDA::Q9HTD7
         (474 letters)



>FitnessBrowser__WCS417:GFF5496
          Length = 474

 Score =  827 bits (2137), Expect = 0.0
 Identities = 427/474 (90%), Positives = 443/474 (93%)

Query: 1   MSPVASSRIEKDLLGTLEVPADAYYGIQTLRAVNNFRLSGVPLSHYPKLVVALAMVKQAA 60
           MS  AS R EKDLLG LEVPA AYYGIQTLRAVNNFRLSGVP+SHYPKLVV LAMVKQAA
Sbjct: 1   MSSAASFRTEKDLLGVLEVPAQAYYGIQTLRAVNNFRLSGVPISHYPKLVVGLAMVKQAA 60

Query: 61  ADANRQLGHLPEDKHAAISEACARLIRGDFHEQFVVDMIQGGAGTSTNMNANEVIANIAL 120
           ADANR+LG L E KHAAISEACARLIRGDFHE+FVVDMIQGGAGTSTNMNANEVIANIAL
Sbjct: 61  ADANRELGQLSEAKHAAISEACARLIRGDFHEEFVVDMIQGGAGTSTNMNANEVIANIAL 120

Query: 121 EAMGHTKGEYKYLHPNNDVNMAQSTNDAYPTAIRLGLLLGHDTLLASLDSLIQAFAAKGV 180
           EAMGH KGEY+YLHPNNDVNMAQSTNDAYPTAIRLGLLLGHD LLASLDSLIQAFAAKG 
Sbjct: 121 EAMGHNKGEYQYLHPNNDVNMAQSTNDAYPTAIRLGLLLGHDALLASLDSLIQAFAAKGE 180

Query: 181 EFAGVLKMGRTQLQDAVPMTLGQEFHAFATTLGEDLDRLRRLAPELLTEVNLGGTAIGTG 240
           EF+ VLKMGRTQLQDAVPMTLGQEF AFATTLGEDL RL+ LAPELLTEVNLGGTAIGTG
Sbjct: 181 EFSHVLKMGRTQLQDAVPMTLGQEFRAFATTLGEDLARLKTLAPELLTEVNLGGTAIGTG 240

Query: 241 INADPGYQKLAVERLAAISGQPLKPAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDL 300
           INADP YQ LAV+RLA ISGQP+ PAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDL
Sbjct: 241 INADPRYQALAVQRLAVISGQPVVPAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDL 300

Query: 301 RLLSSGPRTGINEINLPPRQPGSSIMPGKVNPVIPEAVNQVAFEVIGNDLALTLAAEGGQ 360
           RLLSSGPRTGINEINLP RQPGSSIMPGKVNPVIPEAVNQVAF+VIGNDLALT+AAEGGQ
Sbjct: 301 RLLSSGPRTGINEINLPARQPGSSIMPGKVNPVIPEAVNQVAFQVIGNDLALTMAAEGGQ 360

Query: 361 LQLNVMEPLIAYKIFDSIRLLQRAMDMLREHCITGITANVERCHELVEHSIGLVTALNPY 420
           LQLNVMEPLIA+KIFDSIRLLQRAMDMLREHCI GITAN  RC ELVEHSIGLVTALNPY
Sbjct: 361 LQLNVMEPLIAFKIFDSIRLLQRAMDMLREHCIVGITANEARCRELVEHSIGLVTALNPY 420

Query: 421 IGYENSTRIAKTALESGRGVLELVREEKLLDEATLADILLPENMIAPRLIPLRA 474
           IGYEN+TRIA+ ALESGRGVLELVREE LLD+A L DIL PENMIAPRL+PL+A
Sbjct: 421 IGYENATRIARIALESGRGVLELVREEGLLDDAMLDDILRPENMIAPRLVPLKA 474


Lambda     K      H
   0.318    0.135    0.380 

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: 812
Number of extensions: 21
Number of successful extensions: 2
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: 474
Length of database: 474
Length adjustment: 33
Effective length of query: 441
Effective length of database: 441
Effective search space:   194481
Effective search space used:   194481
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: 51 (24.3 bits)

Align candidate GFF5496 PS417_28130 (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.18320.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     1e-210  686.5   0.1   1.2e-210  686.3   0.1    1.0  1  lcl|FitnessBrowser__WCS417:GFF5496  PS417_28130 aspartate ammonia-ly


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF5496  PS417_28130 aspartate ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  686.3   0.1  1.2e-210  1.2e-210       1     460 [.       8     468 ..       8     473 .. 0.99

  Alignments for each domain:
  == domain 1  score: 686.3 bits;  conditional E-value: 1.2e-210
                           TIGR00839   1 riekdllGekeveaevyyGiqtlrasenfaisnekisdvpefvkalvlvkkaaalanvelkaidekiakaivaac 75 
                                         r ekdllG  ev+a++yyGiqtlra++nf +s++ is++p++v +l++vk+aaa an el++++e    ai +ac
  lcl|FitnessBrowser__WCS417:GFF5496   8 RTEKDLLGVLEVPAQAYYGIQTLRAVNNFRLSGVPISHYPKLVVGLAMVKQAAADANRELGQLSEAKHAAISEAC 82 
                                         89************************************************************************* PP

                           TIGR00839  76 deileGkyldqfivdviqGGaGtsvnmntnevianlalellGhkkGeyqflnpndhvnksqstndayptalkiav 150
                                           ++ G ++++f+vd+iqGGaGts+nmn+nevian+ale +Gh+kGeyq+l+pn+ vn++qstndaypta+++ +
  lcl|FitnessBrowser__WCS417:GFF5496  83 ARLIRGDFHEEFVVDMIQGGAGTSTNMNANEVIANIALEAMGHNKGEYQYLHPNNDVNMAQSTNDAYPTAIRLGL 157
                                         *************************************************************************** PP

                           TIGR00839 151 yesleklvdkiealrdafeqkakefadvlkmGrtqlqdavpltlGqefeayalllerdvkrikr.trelllevnl 224
                                         +     l++++++l +af+ k +ef +vlkmGrtqlqdavp+tlGqef+a+a  l +d+ r+k  + ell evnl
  lcl|FitnessBrowser__WCS417:GFF5496 158 LLGHDALLASLDSLIQAFAAKGEEFSHVLKMGRTQLQDAVPMTLGQEFRAFATTLGEDLARLKTlAPELLTEVNL 232
                                         **************************************************************98355899***** PP

                           TIGR00839 225 GataiGtGlnadkeysklvvkklaevtGlplvpaenlieatsdtgayvevsgalkriavklskvcndlrllssGp 299
                                         G+taiGtG+nad+ y+ l+v++la ++G p+vpa +lieatsd ga+v  sg lkr+avklsk+cndlrllssGp
  lcl|FitnessBrowser__WCS417:GFF5496 233 GGTAIGTGINADPRYQALAVQRLAVISGQPVVPAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDLRLLSSGP 307
                                         *************************************************************************** PP

                           TIGR00839 300 raGlneinlpelqaGssimpakvnpvvpevvnqvcfkviGndttvtlaaeaGqlqlnvlepviafallesisilt 374
                                         r+G+neinlp++q+Gssimp+kvnpv+pe vnqv+f+viGnd ++t+aae+Gqlqlnv+ep+iaf++++si +l+
  lcl|FitnessBrowser__WCS417:GFF5496 308 RTGINEINLPARQPGSSIMPGKVNPVIPEAVNQVAFQVIGNDLALTMAAEGGQLQLNVMEPLIAFKIFDSIRLLQ 382
                                         *************************************************************************** PP

                           TIGR00839 375 naiesltdkcveGitanekicedyvfnsiGivtalnpfiGyekaalvakeaiktgksvrdvvlekdllteeeldd 449
                                         +a+  l+++c+ Gitane +c++ v++siG+vtalnp+iGye+a ++a++a+++g++v ++v e++ll ++ ldd
  lcl|FitnessBrowser__WCS417:GFF5496 383 RAMDMLREHCIVGITANEARCRELVEHSIGLVTALNPYIGYENATRIARIALESGRGVLELVREEGLLDDAMLDD 457
                                         *************************************************************************** PP

                           TIGR00839 450 ilsvenllkpa 460
                                         il++en++ p 
  lcl|FitnessBrowser__WCS417:GFF5496 458 ILRPENMIAPR 468
                                         ********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (468 nodes)
Target sequences:                          1  (474 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: 7.02
//
[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:

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