Alignments for a candidate for ech in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Magnetospirillum magneticum AMB-1

Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (uncharacterized)
to candidate WP_011382625.1 AMB_RS00905 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase

Query= curated2:P24162
         (257 letters)



>NCBI__GCF_000009985.1:WP_011382625.1
          Length = 261

 Score =  224 bits (570), Expect = 2e-63
 Identities = 120/249 (48%), Positives = 163/249 (65%), Gaps = 5/249 (2%)

Query: 14  LAVITLDRPEVMNALNAAMRHELTAAL-HRARGEARAIVLTGSGRAFCSGQDLGDGAAEG 72
           +  ITL+RP  +NA N  M   L +A+ H A    R +V+TG+G+ FC+GQDL D  ++ 
Sbjct: 13  VTTITLNRPGRINAFNVEMHGALRSAVAHAAEDGTRCLVITGAGKGFCAGQDLSDRVSKP 72

Query: 73  ----LNLETVLREEYEPLLQAIYSCPLPVLAAVNGAAAGAGANLALAADVVIAAQSAAFM 128
                +L   L   Y PL++++ + P+PV+AAVNG AAGAGANLALA D+V+AA+SAAF+
Sbjct: 73  GDPPPDLGASLDARYNPLIRSLKALPMPVIAAVNGTAAGAGANLALACDIVVAARSAAFV 132

Query: 129 QAFTRIGLMPDAGGTWWLPRQVGMARAMGMALFAEKIGAEEAARMGLIWEAVPDVDFEHH 188
           Q+F ++GL+PD+GGTW LPR VG ARA  + +  EK+ AE+A + G+IW  V D      
Sbjct: 133 QSFCKVGLIPDSGGTWTLPRLVGTARATALMMLGEKVTAEQAMQWGMIWRCVDDEQLLPT 192

Query: 189 WRARAAHLARGPSAAFAAVKKAFHAGLSNPLPAQLALEARLQGELGQSADFREGVQAFLE 248
             A AA LA  P+   A +KKA     +N L AQL LE  LQ E G + D++EGV+AF+E
Sbjct: 193 VLAMAAQLAAQPTRGLALMKKALARSGANTLDAQLDLERDLQTEAGCTQDYQEGVRAFME 252

Query: 249 KRPPHFTGR 257
           KRPP F GR
Sbjct: 253 KRPPRFEGR 261


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: 153
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: 261
Length adjustment: 24
Effective length of query: 233
Effective length of database: 237
Effective search space:    55221
Effective search space used:    55221
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 WP_011382625.1 AMB_RS00905 (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.27751.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     9e-120  384.9   2.4     1e-119  384.8   2.4    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011382625.1  AMB_RS00905 2-(1,2-epoxy-1,2-dih


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011382625.1  AMB_RS00905 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 !  384.8   2.4    1e-119    1e-119       1     256 []       5     261 .]       5     261 .] 0.99

  Alignments for each domain:
  == domain 1  score: 384.8 bits;  conditional E-value: 1e-119
                                 TIGR02280   1 illelekgvlrltlnrpdklnsfteemhaelaealerverddvrallltGaGrGfcaGqdlsernvtkg 69 
                                               il++  + v ++tlnrp ++n+f+ emh +l+ a+ ++  d+ r+l++tGaG+GfcaGqdls+r  ++g
  lcl|NCBI__GCF_000009985.1:WP_011382625.1   5 ILVARTGDVTTITLNRPGRINAFNVEMHGALRSAVAHAAEDGTRCLVITGAGKGFCAGQDLSDRVSKPG 73 
                                               67788899************************************************************9 PP

                                 TIGR02280  70 .aapdlGetvekfynplvrrlaalpkpvvvavnGvaaGaGanlalagdivlaaesakfiqafaklGlip 137
                                                ++pdlG +++  ynpl+r l+alp+pv++avnG aaGaGanlala+div+aa+sa f+q+f+k+Glip
  lcl|NCBI__GCF_000009985.1:WP_011382625.1  74 dPPPDLGASLDARYNPLIRSLKALPMPVIAAVNGTAAGAGANLALACDIVVAARSAAFVQSFCKVGLIP 142
                                               899****************************************************************** PP

                                 TIGR02280 138 dsGGtwllprlvGrarakglallgekldaetaaewGliwqvvddealadevqalaahlakqptrglali 206
                                               dsGGtw+lprlvG+ara++l +lgek+ ae+a++wG+iw++vdde+l  +v a+aa+la+qptrglal+
  lcl|NCBI__GCF_000009985.1:WP_011382625.1 143 DSGGTWTLPRLVGTARATALMMLGEKVTAEQAMQWGMIWRCVDDEQLLPTVLAMAAQLAAQPTRGLALM 211
                                               ********************************************************************* PP

                                 TIGR02280 207 kralqaaetnsldtqldlerdlqrelGrsadyaeGvaafldkrepefkGk 256
                                               k+al  + +n+ld+qldlerdlq e+G ++dy+eGv af++kr p+f+G+
  lcl|NCBI__GCF_000009985.1:WP_011382625.1 212 KKALARSGANTLDAQLDLERDLQTEAGCTQDYQEGVRAFMEKRPPRFEGR 261
                                               ************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (256 nodes)
Target sequences:                          1  (261 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 8.65
//
[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, or view the source code.

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