Alignments for a candidate for aspA in Rhizobium etli CFN 42

GapMind for catabolism of small carbon sources

Alignments for a candidate for aspA in Rhizobium etli CFN 42

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate WP_011428205.1 RHE_RS25855 aspartate ammonia-lyase

Query= BRENDA::Q0PC50
         (468 letters)



>NCBI__GCF_000092045.1:WP_011428205.1
          Length = 475

 Score =  545 bits (1405), Expect = e-160
 Identities = 279/459 (60%), Positives = 337/459 (73%)

Query: 4   RKEHDFIGELEISDEVYYGVQTFRAVENFDISHDRLKDFPRFVRALARVKKAAAMANHEL 63
           R EHD IG+ ++    YYGV T RAVENF I+   LK+    + +LA +K+AAA  N  L
Sbjct: 10  RVEHDLIGDRDVPASAYYGVHTVRAVENFPITGQTLKESADLIASLAAIKQAAAEVNVSL 69

Query: 64  GLLDKNIQDAIIKACDKILEGGYYDQFVVDMIQGGAGTSTNMNANEVIANIGLELMGHKK 123
           GLLD+   DAI+ AC +I +G  +DQFVVD+IQGGAGTSTNMNANEVIAN  LE++GH++
Sbjct: 70  GLLDQQRADAIVAACIEIRDGALHDQFVVDLIQGGAGTSTNMNANEVIANRALEILGHRR 129

Query: 124 GEYQYLHPNDHVNLSQSTNDAYPTALHLALHDYLSDLAKAMEHLKKAYERKAEEFKDVLK 183
           GEYQ+LHPN+HVNLSQSTND YPTAL LA    +  L  AM  L++A+  KA EF DVLK
Sbjct: 130 GEYQHLHPNEHVNLSQSTNDVYPTALKLAAWIGVHRLVDAMAILRRAFAAKAVEFADVLK 189

Query: 184 MGRTQLQDAVPMTLGREFKTFAVMIGEDIQRVLEARKLILEINLGGTAIGTGINSHPDYP 243
           MGRTQLQDAVPMTLG+EF T+A+M+ ED  R+LEA  LI EINLG TAIGTGI +HP Y 
Sbjct: 190 MGRTQLQDAVPMTLGQEFGTYALMLAEDEARLLEAVSLIREINLGATAIGTGITAHPHYA 249

Query: 244 KVVERKIREVTGFEYTVAEDLIEATQDTGAYVQISGVLKRVATKLSKVCNDLRLLSSGPK 303
            +V  ++  + G +   + DL+EATQD G++VQ+SGVLKRVA KLSK CNDLRLLSSGP+
Sbjct: 250 ALVRERLSAIVGIDLVTSPDLVEATQDCGSFVQLSGVLKRVAVKLSKTCNDLRLLSSGPR 309

Query: 304 CGLNEINLPKMQPGSSIMPGKVNPVIPEVVNQVCYFVIGADVTVTFACEGGQLQLNVFEP 363
            GLNEINLP  Q GSSIMPGKVNPVIPEVVNQV + VIG DVT+T A E GQLQLN FEP
Sbjct: 310 AGLNEINLPARQAGSSIMPGKVNPVIPEVVNQVAFEVIGNDVTITMAAEAGQLQLNAFEP 369

Query: 364 VVAYSLFNSVVMLEKAMYTLADKCIDGITANEKICSDFVYNSVGIVTALNPYIGYENSAS 423
           V+ YSL+ S+  L  A  TL   CI GITAN       V  S+GIVTALNPYIGY N+  
Sbjct: 370 VIFYSLYRSLSHLTNACLTLEANCIRGITANRDRLRQTVEQSIGIVTALNPYIGYRNATE 429

Query: 424 IAKEAMNTGKRVADIALERGLLSKEQIDEILTPSNMLNP 462
           +A EA ++G+ V +I LERGL+ KE +D +L P  +  P
Sbjct: 430 VALEAHHSGRGVYEILLERGLMQKEHLDAVLRPETLTRP 468


Lambda     K      H
   0.318    0.135    0.383 

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: 578
Number of extensions: 15
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: 468
Length of database: 475
Length adjustment: 33
Effective length of query: 435
Effective length of database: 442
Effective search space:   192270
Effective search space used:   192270
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 WP_011428205.1 RHE_RS25855 (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.2680813.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-214  698.6   0.2   2.6e-214  698.3   0.2    1.0  1  NCBI__GCF_000092045.1:WP_011428205.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000092045.1:WP_011428205.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  698.3   0.2  2.6e-214  2.6e-214       1     462 [.      10     471 ..      10     474 .. 1.00

  Alignments for each domain:
  == domain 1  score: 698.3 bits;  conditional E-value: 2.6e-214
                             TIGR00839   1 riekdllGekeveaevyyGiqtlrasenfaisnekisdvpefvkalvlvkkaaalanvelkaidekiakaiva 73 
                                           r+e+dl+G+++v+a +yyG++t+ra+enf+i+++++++  +++ +l+ +k+aaa  nv l+++d++ a aiva
  NCBI__GCF_000092045.1:WP_011428205.1  10 RVEHDLIGDRDVPASAYYGVHTVRAVENFPITGQTLKESADLIASLAAIKQAAAEVNVSLGLLDQQRADAIVA 82 
                                           89*********************************************************************** PP

                             TIGR00839  74 acdeileGkyldqfivdviqGGaGtsvnmntnevianlalellGhkkGeyqflnpndhvnksqstndayptal 146
                                           ac ei +G ++dqf+vd+iqGGaGts+nmn+nevian+ale+lGh++Geyq+l+pn+hvn sqstnd+yptal
  NCBI__GCF_000092045.1:WP_011428205.1  83 ACIEIRDGALHDQFVVDLIQGGAGTSTNMNANEVIANRALEILGHRRGEYQHLHPNEHVNLSQSTNDVYPTAL 155
                                           ************************************************************************* PP

                             TIGR00839 147 kiavyesleklvdkiealrdafeqkakefadvlkmGrtqlqdavpltlGqefeayalllerdvkrikrtrell 219
                                           k+a +  +++lvd++  lr af+ ka+efadvlkmGrtqlqdavp+tlGqef +yal+l +d  r+ ++  l+
  NCBI__GCF_000092045.1:WP_011428205.1 156 KLAAWIGVHRLVDAMAILRRAFAAKAVEFADVLKMGRTQLQDAVPMTLGQEFGTYALMLAEDEARLLEAVSLI 228
                                           ************************************************************************* PP

                             TIGR00839 220 levnlGataiGtGlnadkeysklvvkklaevtGlplvpaenlieatsdtgayvevsgalkriavklskvcndl 292
                                           +e+nlGataiGtG+ a+++y+ lv  +l+ + G+ lv++ +l+eat+d+g++v++sg+lkr+avklsk cndl
  NCBI__GCF_000092045.1:WP_011428205.1 229 REINLGATAIGTGITAHPHYAALVRERLSAIVGIDLVTSPDLVEATQDCGSFVQLSGVLKRVAVKLSKTCNDL 301
                                           ************************************************************************* PP

                             TIGR00839 293 rllssGpraGlneinlpelqaGssimpakvnpvvpevvnqvcfkviGndttvtlaaeaGqlqlnvlepviafa 365
                                           rllssGpraGlneinlp++qaGssimp+kvnpv+pevvnqv+f+viGnd t+t+aaeaGqlqln +epvi ++
  NCBI__GCF_000092045.1:WP_011428205.1 302 RLLSSGPRAGLNEINLPARQAGSSIMPGKVNPVIPEVVNQVAFEVIGNDVTITMAAEAGQLQLNAFEPVIFYS 374
                                           ************************************************************************* PP

                             TIGR00839 366 llesisiltnaiesltdkcveGitanekicedyvfnsiGivtalnpfiGyekaalvakeaiktgksvrdvvle 438
                                           l++s+s ltna+ +l  +c+ Gitan++++++ v++siGivtalnp+iGy++a  va ea ++g++v+++ le
  NCBI__GCF_000092045.1:WP_011428205.1 375 LYRSLSHLTNACLTLEANCIRGITANRDRLRQTVEQSIGIVTALNPYIGYRNATEVALEAHHSGRGVYEILLE 447
                                           ************************************************************************* PP

                             TIGR00839 439 kdllteeelddilsvenllkpayk 462
                                           ++l+ +e+ld +l++e l++p+ k
  NCBI__GCF_000092045.1:WP_011428205.1 448 RGLMQKEHLDAVLRPETLTRPSEK 471
                                           *********************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (468 nodes)
Target sequences:                          1  (475 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 28.32
//
[ok]

This GapMind analysis is from Apr 09 2024. 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