Alignments for a candidate for ech in Sinorhizobium fredii NGR234

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Sinorhizobium fredii NGR234

Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (uncharacterized)
to candidate YP_002827119.1 NGR_c26090 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase

Query= curated2:P24162
         (257 letters)



>NCBI__GCF_000018545.1:YP_002827119.1
          Length = 263

 Score =  221 bits (562), Expect = 2e-62
 Identities = 126/262 (48%), Positives = 161/262 (61%), Gaps = 13/262 (4%)

Query: 5   TIRYEISEGLAVITLDRPEVMNALNAAMRHELTAALHRARGE--ARAIVLTGSGRAFCSG 62
           T+   + +G+  +TL+RP+ +NA N AM   L A   RA  +   RA++LTG+GR F +G
Sbjct: 6   TVLSALEDGVLRLTLNRPDKLNAFNEAMHVALRAGFERAHSDDHVRAVLLTGAGRGFSAG 65

Query: 63  QDLGD------GAAE-GLNLETVLREEYEPLLQAIYSCPLPVLAAVNGAAAGAGANLALA 115
           QDLGD      G  + G  +ET     Y PLL+ I +   PV+ AVNG AAGAGAN+A A
Sbjct: 66  QDLGDRDPRKGGTPDLGQTIETF----YNPLLRLIRNLEKPVVCAVNGVAAGAGANIAFA 121

Query: 116 ADVVIAAQSAAFMQAFTRIGLMPDAGGTWWLPRQVGMARAMGMALFAEKIGAEEAARMGL 175
            D+ +AA+SA F+QAF +IGL+PD+GGTW L R +G ARA  +AL AE + AE AA  GL
Sbjct: 122 CDITLAARSARFIQAFAKIGLVPDSGGTWSLSRLIGEARAKALALTAEPLDAETAASWGL 181

Query: 176 IWEAVPDVDFEHHWRARAAHLARGPSAAFAAVKKAFHAGLSNPLPAQLALEARLQGELGQ 235
           IW A+ D        A AA LA GP+      K+A  A  +N    QL LE  LQ E G+
Sbjct: 182 IWRAIDDAALLDEATALAARLAAGPTKGIGLTKRAIQAAANNAFDEQLDLERDLQREAGR 241

Query: 236 SADFREGVQAFLEKRPPHFTGR 257
           SAD+ EGV AFLEKR P F GR
Sbjct: 242 SADYAEGVAAFLEKRKPEFKGR 263


Lambda     K      H
   0.321    0.133    0.397 

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: 158
Number of extensions: 7
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: 257
Length of database: 263
Length adjustment: 24
Effective length of query: 233
Effective length of database: 239
Effective search space:    55687
Effective search space used:    55687
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 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate YP_002827119.1 NGR_c26090 (2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase)
to HMM TIGR02280 (paaB: phenylacetate degradation probable enoyl-CoA hydratase PaaB (EC 4.2.1.17))

# 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/TIGR02280.hmm
# target sequence database:        /tmp/gapView.1639.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02280  [M=256]
Accession:   TIGR02280
Description: PaaB1: phenylacetate degradation probable enoyl-CoA hydratase PaaB
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.9e-137  442.2   5.1   3.3e-137  442.1   5.1    1.0  1  lcl|NCBI__GCF_000018545.1:YP_002827119.1  NGR_c26090 2-(1,2-epoxy-1,2-dihy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000018545.1:YP_002827119.1  NGR_c26090 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.1   5.1  3.3e-137  3.3e-137       1     256 []       7     263 .]       7     263 .] 1.00

  Alignments for each domain:
  == domain 1  score: 442.1 bits;  conditional E-value: 3.3e-137
                                 TIGR02280   1 illelekgvlrltlnrpdklnsfteemhaelaealerverdd.vrallltGaGrGfcaGqdlsernvtk 68 
                                               +l++le+gvlrltlnrpdkln+f+e mh +l++++er+++dd vra+lltGaGrGf+aGqdl++r+++k
  lcl|NCBI__GCF_000018545.1:YP_002827119.1   7 VLSALEDGVLRLTLNRPDKLNAFNEAMHVALRAGFERAHSDDhVRAVLLTGAGRGFSAGQDLGDRDPRK 75 
                                               799**************************************99************************** PP

                                 TIGR02280  69 gaapdlGetvekfynplvrrlaalpkpvvvavnGvaaGaGanlalagdivlaaesakfiqafaklGlip 137
                                               g++pdlG+t+e+fynpl+r++++l+kpvv+avnGvaaGaGan+a+a+di+laa+sa+fiqafak+Gl+p
  lcl|NCBI__GCF_000018545.1:YP_002827119.1  76 GGTPDLGQTIETFYNPLLRLIRNLEKPVVCAVNGVAAGAGANIAFACDITLAARSARFIQAFAKIGLVP 144
                                               ********************************************************************* PP

                                 TIGR02280 138 dsGGtwllprlvGrarakglallgekldaetaaewGliwqvvddealadevqalaahlakqptrglali 206
                                               dsGGtw+l rl+G+arak+lal++e+ldaetaa+wGliw+++dd+al de+ alaa+la++pt+g++l+
  lcl|NCBI__GCF_000018545.1:YP_002827119.1 145 DSGGTWSLSRLIGEARAKALALTAEPLDAETAASWGLIWRAIDDAALLDEATALAARLAAGPTKGIGLT 213
                                               ********************************************************************* PP

                                 TIGR02280 207 kralqaaetnsldtqldlerdlqrelGrsadyaeGvaafldkrepefkGk 256
                                               kra+qaa+ n++d+qldlerdlqre+GrsadyaeGvaafl+kr+pefkG+
  lcl|NCBI__GCF_000018545.1:YP_002827119.1 214 KRAIQAAANNAFDEQLDLERDLQREAGRSADYAEGVAAFLEKRKPEFKGR 263
                                               ************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (256 nodes)
Target sequences:                          1  (263 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: 00:00:00.01
# Mc/sec: 6.22
//
[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