Alignments for a candidate for fadA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Klebsiella michiganensis M5al

Align 3-ketoacyl-CoA thiolase FadA; Acetyl-CoA acyltransferase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 (characterized)
to candidate BWI76_RS01360 BWI76_RS01360 acetyl-CoA C-acyltransferase FadA

Query= SwissProt::P21151
         (387 letters)



>FitnessBrowser__Koxy:BWI76_RS01360
          Length = 387

 Score =  716 bits (1848), Expect = 0.0
 Identities = 358/387 (92%), Positives = 373/387 (96%)

Query: 1   MEQVVIVDAIRTPMGRSKGGAFRNVRAEDLSAHLMRSLLARNPALEAAALDDIYWGCVQQ 60
           MEQVVIVDA+RTPMGRSKGGAFR+VRA+DLSAHLMRSLL+RNP+LEA+A+DDIYWGCVQQ
Sbjct: 1   MEQVVIVDAVRTPMGRSKGGAFRHVRADDLSAHLMRSLLSRNPSLEASAIDDIYWGCVQQ 60

Query: 61  TLEQGFNIARNAALLAEVPHSVPAVTVNRLCGSSMQALHDAARMIMTGDAQACLVGGVEH 120
           TLEQGFNIARNAALLAE+PHSVPA TVNRLCGSSMQALHDAARMIMTGDA  CL+GGVEH
Sbjct: 61  TLEQGFNIARNAALLAEIPHSVPATTVNRLCGSSMQALHDAARMIMTGDASVCLIGGVEH 120

Query: 121 MGHVPMSHGVDFHPGLSRNVAKAAGMMGLTAEMLARMHGISREMQDAFAARSHARAWAAT 180
           MGHVPMSHGVDFHPGLSRNVAKAAGMMGLTAEMLAR+HGISREMQD FAARSHARAWAAT
Sbjct: 121 MGHVPMSHGVDFHPGLSRNVAKAAGMMGLTAEMLARLHGISREMQDQFAARSHARAWAAT 180

Query: 181 QSAAFKNEIIPTGGHDADGVLKQFNYDEVIRPETTVEALATLRPAFDPVNGMVTAGTSSA 240
           QS AFK EIIPTGGHDADGVLK ++YDEVIRPETTVEALA LRPAFDPV G VTAGTSSA
Sbjct: 181 QSGAFKTEIIPTGGHDADGVLKSYSYDEVIRPETTVEALAALRPAFDPVTGTVTAGTSSA 240

Query: 241 LSDGAAAMLVMSESRAHELGLKPRARVRSMAVVGCDPSIMGYGPVPASKLALKKAGLSAS 300
           LSDGAAAML+MSESRA ELGLKPRARVRSMAVVGCDPSIMGYGPVPASKLALKKAGLSAS
Sbjct: 241 LSDGAAAMLLMSESRARELGLKPRARVRSMAVVGCDPSIMGYGPVPASKLALKKAGLSAS 300

Query: 301 DIGVFEMNEAFAAQILPCIKDLGLIEQIDEKINLNGGAIALGHPLGCSGARISTTLLNLM 360
           DI VFEMNEAFAAQILPCIKDLGL+EQIDEKINLNGGAIALGHPLGCSGARISTTL+N M
Sbjct: 301 DIDVFEMNEAFAAQILPCIKDLGLMEQIDEKINLNGGAIALGHPLGCSGARISTTLINQM 360

Query: 361 ERKDVQFGLATMCIGLGQGIATVFERV 387
           ERKD QFGLATMCIGLGQGIATVFERV
Sbjct: 361 ERKDAQFGLATMCIGLGQGIATVFERV 387


Lambda     K      H
   0.320    0.133    0.387 

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: 607
Number of extensions: 14
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: 387
Length of database: 387
Length adjustment: 30
Effective length of query: 357
Effective length of database: 357
Effective search space:   127449
Effective search space used:   127449
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: 50 (23.9 bits)

Align candidate BWI76_RS01360 BWI76_RS01360 (acetyl-CoA C-acyltransferase FadA)
to HMM TIGR02445 (fadA: acetyl-CoA C-acyltransferase FadA (EC 2.3.1.16))

# 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/TIGR02445.hmm
# target sequence database:        /tmp/gapView.15755.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02445  [M=385]
Accession:   TIGR02445
Description: fadA: acetyl-CoA C-acyltransferase FadA
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   4.5e-242  788.7   6.9   5.1e-242  788.5   6.9    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS01360  BWI76_RS01360 acetyl-CoA C-acylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS01360  BWI76_RS01360 acetyl-CoA C-acyltransferase FadA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  788.5   6.9  5.1e-242  5.1e-242       1     385 []       3     387 .]       3     387 .] 1.00

  Alignments for each domain:
  == domain 1  score: 788.5 bits;  conditional E-value: 5.1e-242
                               TIGR02445   1 dvvivdalrtpmgrskggafrntraedlsahllkkllarnpkveaaevediywgcvqqtleqgfniarnaa 71 
                                             +vvivda+rtpmgrskggafr++ra+dlsahl+++ll+rnp +ea++++diywgcvqqtleqgfniarnaa
  lcl|FitnessBrowser__Koxy:BWI76_RS01360   3 QVVIVDAVRTPMGRSKGGAFRHVRADDLSAHLMRSLLSRNPSLEASAIDDIYWGCVQQTLEQGFNIARNAA 73 
                                             79********************************************************************* PP

                               TIGR02445  72 llaevphevaavtvnrlcgssmqalhdaaraimtgdaevcliggvehmghvsmshgvdfhpglskhvakaa 142
                                             llae+ph+v+a tvnrlcgssmqalhdaar+imtgda vcliggvehmghv+mshgvdfhpgls++vakaa
  lcl|FitnessBrowser__Koxy:BWI76_RS01360  74 LLAEIPHSVPATTVNRLCGSSMQALHDAARMIMTGDASVCLIGGVEHMGHVPMSHGVDFHPGLSRNVAKAA 144
                                             *********************************************************************** PP

                               TIGR02445 143 gmmgltaemlgklhgisreqqdafaarsharahaatlegkfkneiiptegydadgvlkvldydevirpett 213
                                             gmmgltaeml++lhgisre+qd+faarshara+aat++g+fk eiipt+g+dadgvlk + ydevirpett
  lcl|FitnessBrowser__Koxy:BWI76_RS01360 145 GMMGLTAEMLARLHGISREMQDQFAARSHARAWAATQSGAFKTEIIPTGGHDADGVLKSYSYDEVIRPETT 215
                                             *********************************************************************** PP

                               TIGR02445 214 vealaalrpafdpkngtvtagtssalsdgasamlvmseeraqelgvkprarirsmavagvdpsimgygpvp 284
                                             vealaalrpafdp++gtvtagtssalsdga+aml+mse+ra+elg+kprar+rsmav+g+dpsimgygpvp
  lcl|FitnessBrowser__Koxy:BWI76_RS01360 216 VEALAALRPAFDPVTGTVTAGTSSALSDGAAAMLLMSESRARELGLKPRARVRSMAVVGCDPSIMGYGPVP 286
                                             *********************************************************************** PP

                               TIGR02445 285 atkkalkraglsisdidvlelneafaaqalpvlkdlglldkldekvnlnggaialghplgcsgaristtll 355
                                             a+k+alk+agls+sdidv+e+neafaaq+lp++kdlgl++++dek+nlnggaialghplgcsgaristtl+
  lcl|FitnessBrowser__Koxy:BWI76_RS01360 287 ASKLALKKAGLSASDIDVFEMNEAFAAQILPCIKDLGLMEQIDEKINLNGGAIALGHPLGCSGARISTTLI 357
                                             *********************************************************************** PP

                               TIGR02445 356 nlmerkdakfglatmciglgqgiatvferv 385
                                             n merkda+fglatmciglgqgiatvferv
  lcl|FitnessBrowser__Koxy:BWI76_RS01360 358 NQMERKDAQFGLATMCIGLGQGIATVFERV 387
                                             *****************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (387 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: 00:00:00.01
# Mc/sec: 11.49
//
[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