Alignments for a candidate for ech in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Klebsiella michiganensis M5al

Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (uncharacterized)
to candidate BWI76_RS13120 BWI76_RS13120 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase

Query= curated2:P24162
         (257 letters)



>FitnessBrowser__Koxy:BWI76_RS13120
          Length = 262

 Score =  226 bits (575), Expect = 5e-64
 Identities = 118/257 (45%), Positives = 164/257 (63%), Gaps = 10/257 (3%)

Query: 9   EISEGLAVITLDRPEVMNALNAAMRHELTAALHRAR--GEARAIVLTGSGRAFCSGQDLG 66
           E+ +G+  ITL+RP+ +N+ N  M  +L A L +A    + R ++LTG+GR FC+GQDL 
Sbjct: 8   EVEQGVMTITLNRPDRLNSFNDLMHQQLAACLKQAERDDDVRCLLLTGAGRGFCAGQDLN 67

Query: 67  D------GAAEGLNLETVLREEYEPLLQAIYSCPLPVLAAVNGAAAGAGANLALAADVVI 120
           D      G A  L L   +   Y PL++ + + P PV+ AVNG AAGAGA LAL  D+V+
Sbjct: 68  DRNVDPSGPAPDLGLS--VERFYNPLVRRLAALPKPVICAVNGVAAGAGATLALGCDIVL 125

Query: 121 AAQSAAFMQAFTRIGLMPDAGGTWWLPRQVGMARAMGMALFAEKIGAEEAARMGLIWEAV 180
           AA+SA F+ AF+++GL+PD GG+W+LPR  G ARAMG+AL  + + AE+AA+ G+IW+ V
Sbjct: 126 AARSAKFVMAFSKLGLVPDCGGSWFLPRVAGRARAMGLALLGDSLSAEQAAQWGMIWQVV 185

Query: 181 PDVDFEHHWRARAAHLARGPSAAFAAVKKAFHAGLSNPLPAQLALEARLQGELGQSADFR 240
            D + +    A A HLA  P+     +KKA     +  L  QL LE   Q   G+SAD+R
Sbjct: 186 DDAELKDTGLALARHLAAQPTYGLGLIKKALQLAETQTLDQQLDLERDYQRLAGRSADYR 245

Query: 241 EGVQAFLEKRPPHFTGR 257
           EGV AFL KRPP F+G+
Sbjct: 246 EGVSAFLAKRPPQFSGK 262


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: 168
Number of extensions: 10
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: 262
Length adjustment: 24
Effective length of query: 233
Effective length of database: 238
Effective search space:    55454
Effective search space used:    55454
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 BWI76_RS13120 BWI76_RS13120 (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.30831.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   1.5e-141  456.3   1.1   1.7e-141  456.1   1.1    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS13120  BWI76_RS13120 2-(1,2-epoxy-1,2-d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS13120  BWI76_RS13120 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 !  456.1   1.1  1.7e-141  1.7e-141       1     256 []       5     262 .]       5     262 .] 0.99

  Alignments for each domain:
  == domain 1  score: 456.1 bits;  conditional E-value: 1.7e-141
                               TIGR02280   1 illelekgvlrltlnrpdklnsfteemhaelaealerverdd.vrallltGaGrGfcaGqdlsernvtkg. 69 
                                             il+e+e+gv+++tlnrpd+lnsf++ mh++la++l+++erdd vr+llltGaGrGfcaGqdl++rnv+++ 
  lcl|FitnessBrowser__Koxy:BWI76_RS13120   5 ILSEVEQGVMTITLNRPDRLNSFNDLMHQQLAACLKQAERDDdVRCLLLTGAGRGFCAGQDLNDRNVDPSg 75 
                                             89**************************************999*************************998 PP

                               TIGR02280  70 aapdlGetvekfynplvrrlaalpkpvvvavnGvaaGaGanlalagdivlaaesakfiqafaklGlipdsG 140
                                             +apdlG +ve+fynplvrrlaalpkpv++avnGvaaGaGa+lal++divlaa+sakf++af+klGl+pd+G
  lcl|FitnessBrowser__Koxy:BWI76_RS13120  76 PAPDLGLSVERFYNPLVRRLAALPKPVICAVNGVAAGAGATLALGCDIVLAARSAKFVMAFSKLGLVPDCG 146
                                             9********************************************************************** PP

                               TIGR02280 141 GtwllprlvGrarakglallgekldaetaaewGliwqvvddealadevqalaahlakqptrglalikralq 211
                                             G+w+lpr++Grara+glallg+ l+ae+aa+wG+iwqvvdd++l+d+  ala+hla+qpt gl+lik+alq
  lcl|FitnessBrowser__Koxy:BWI76_RS13120 147 GSWFLPRVAGRARAMGLALLGDSLSAEQAAQWGMIWQVVDDAELKDTGLALARHLAAQPTYGLGLIKKALQ 217
                                             *********************************************************************** PP

                               TIGR02280 212 aaetnsldtqldlerdlqrelGrsadyaeGvaafldkrepefkGk 256
                                              aet++ld+qldlerd+qr +Grsady+eGv+afl+kr p+f Gk
  lcl|FitnessBrowser__Koxy:BWI76_RS13120 218 LAETQTLDQQLDLERDYQRLAGRSADYREGVSAFLAKRPPQFSGK 262
                                             *******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (256 nodes)
Target sequences:                          1  (262 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: 00:00:00.00
# Mc/sec: 7.69
//
[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