Alignments for a candidate for aspA in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for aspA in Pseudomonas fluorescens FW300-N1B4

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate Pf1N1B4_2025 Aspartate ammonia-lyase (EC 4.3.1.1)

Query= BRENDA::Q9HTD7
         (474 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2025
          Length = 474

 Score =  831 bits (2147), Expect = 0.0
 Identities = 428/474 (90%), Positives = 444/474 (93%)

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

Query: 61  ADANRQLGHLPEDKHAAISEACARLIRGDFHEQFVVDMIQGGAGTSTNMNANEVIANIAL 120
           ADANR+LGHL E KHAAISEACARLIRGDFHE+FVVDMIQGGAGTSTNMNANEVIANIAL
Sbjct: 61  ADANRELGHLSEAKHAAISEACARLIRGDFHEEFVVDMIQGGAGTSTNMNANEVIANIAL 120

Query: 121 EAMGHTKGEYKYLHPNNDVNMAQSTNDAYPTAIRLGLLLGHDTLLASLDSLIQAFAAKGV 180
           EAMGH+KGEY+YLHPNNDVNMAQSTNDAYPTAIRLGLLLGHD LLASLDSLIQ+FAAKG 
Sbjct: 121 EAMGHSKGEYQYLHPNNDVNMAQSTNDAYPTAIRLGLLLGHDALLASLDSLIQSFAAKGQ 180

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

Query: 241 INADPGYQKLAVERLAAISGQPLKPAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDL 300
           INADP YQ LAV+RLA ISG PL PAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDL
Sbjct: 241 INADPRYQHLAVQRLATISGHPLVPAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDL 300

Query: 301 RLLSSGPRTGINEINLPPRQPGSSIMPGKVNPVIPEAVNQVAFEVIGNDLALTLAAEGGQ 360
           RLLSSGPRTGINEINLP RQPGSSIMPGKVNPVIPEAVNQVAF++IGNDLALT+AAEGGQ
Sbjct: 301 RLLSSGPRTGINEINLPARQPGSSIMPGKVNPVIPEAVNQVAFQIIGNDLALTIAAEGGQ 360

Query: 361 LQLNVMEPLIAYKIFDSIRLLQRAMDMLREHCITGITANVERCHELVEHSIGLVTALNPY 420
           LQLNVMEPLIA+KIFDSIRLLQRAMDMLREHCI GITAN ERC ELVEHSIGLVTALNPY
Sbjct: 361 LQLNVMEPLIAFKIFDSIRLLQRAMDMLREHCIVGITANEERCRELVEHSIGLVTALNPY 420

Query: 421 IGYENSTRIAKTALESGRGVLELVREEKLLDEATLADILLPENMIAPRLIPLRA 474
           IGYEN+TRIA+ ALESGRGVLELVREE LLDE  LADIL PENMIAPRL+PL+A
Sbjct: 421 IGYENATRIARIALESGRGVLELVREEGLLDEEMLADILRPENMIAPRLVPLKA 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: 818
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 Pf1N1B4_2025 (Aspartate ammonia-lyase (EC 4.3.1.1))
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.10932.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   8.1e-211  686.8   0.0   9.5e-211  686.6   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2025  Aspartate ammonia-lyase (EC 4.3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2025  Aspartate ammonia-lyase (EC 4.3.1.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  686.6   0.0  9.5e-211  9.5e-211       1     460 [.       8     468 ..       8     473 .. 0.99

  Alignments for each domain:
  == domain 1  score: 686.6 bits;  conditional E-value: 9.5e-211
                                      TIGR00839   1 riekdllGekeveaevyyGiqtlrasenfaisnekisdvpefvkalvlvkkaaalanvelkaid 64 
                                                    r ekdllG  ev+a++yyGiqtlra++nf +s++ is++p++v +l++vk+aaa an el++++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2025   8 RTEKDLLGVLEVPAQAYYGIQTLRAVNNFRLSGVPISHYPKLVVGLAMVKQAAADANRELGHLS 71 
                                                    89************************************************************** PP

                                      TIGR00839  65 ekiakaivaacdeileGkyldqfivdviqGGaGtsvnmntnevianlalellGhkkGeyqflnp 128
                                                    e    ai +ac  ++ G ++++f+vd+iqGGaGts+nmn+nevian+ale +Gh kGeyq+l+p
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2025  72 EAKHAAISEACARLIRGDFHEEFVVDMIQGGAGTSTNMNANEVIANIALEAMGHSKGEYQYLHP 135
                                                    **************************************************************** PP

                                      TIGR00839 129 ndhvnksqstndayptalkiavyesleklvdkiealrdafeqkakefadvlkmGrtqlqdavpl 192
                                                    n+ vn++qstndaypta+++ ++     l++++++l ++f+ k +ef++vlkmGrtqlqdavp+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2025 136 NNDVNMAQSTNDAYPTAIRLGLLLGHDALLASLDSLIQSFAAKGQEFNHVLKMGRTQLQDAVPM 199
                                                    **************************************************************** PP

                                      TIGR00839 193 tlGqefeayalllerdvkrikr.trelllevnlGataiGtGlnadkeysklvvkklaevtGlpl 255
                                                    tlGqef+a+a  l +d+ r+k  + ell evnlG+taiGtG+nad+ y++l+v++la ++G pl
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2025 200 TLGQEFRAFATTLGEDLARLKTlAPELLTEVNLGGTAIGTGINADPRYQHLAVQRLATISGHPL 263
                                                    ********************98355899************************************ PP

                                      TIGR00839 256 vpaenlieatsdtgayvevsgalkriavklskvcndlrllssGpraGlneinlpelqaGssimp 319
                                                    vpa +lieatsd ga+v  sg lkr+avklsk+cndlrllssGpr+G+neinlp++q+Gssimp
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2025 264 VPAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDLRLLSSGPRTGINEINLPARQPGSSIMP 327
                                                    **************************************************************** PP

                                      TIGR00839 320 akvnpvvpevvnqvcfkviGndttvtlaaeaGqlqlnvlepviafallesisiltnaiesltdk 383
                                                    +kvnpv+pe vnqv+f++iGnd ++t+aae+Gqlqlnv+ep+iaf++++si +l++a+  l+++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2025 328 GKVNPVIPEAVNQVAFQIIGNDLALTIAAEGGQLQLNVMEPLIAFKIFDSIRLLQRAMDMLREH 391
                                                    **************************************************************** PP

                                      TIGR00839 384 cveGitanekicedyvfnsiGivtalnpfiGyekaalvakeaiktgksvrdvvlekdllteeel 447
                                                    c+ Gitane++c++ v++siG+vtalnp+iGye+a ++a++a+++g++v ++v e++ll ee l
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2025 392 CIVGITANEERCRELVEHSIGLVTALNPYIGYENATRIARIALESGRGVLELVREEGLLDEEML 455
                                                    **************************************************************** PP

                                      TIGR00839 448 ddilsvenllkpa 460
                                                     dil++en++ p 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2025 456 ADILRPENMIAPR 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: 00:00:00.02
# Mc/sec: 7.75
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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