Alignments for a candidate for patD in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for patD in Escherichia coli BW25113

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 15565 b1444 medium chain aldehyde dehydrogenase (NCBI)

Query= BRENDA::P77674
         (474 letters)



>FitnessBrowser__Keio:15565
          Length = 474

 Score =  949 bits (2454), Expect = 0.0
 Identities = 474/474 (100%), Positives = 474/474 (100%)

Query: 1   MQHKLLINGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTP 60
           MQHKLLINGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTP
Sbjct: 1   MQHKLLINGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTP 60

Query: 61  KVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG 120
           KVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG
Sbjct: 61  KVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG 120

Query: 121 LAAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLT 180
           LAAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLT
Sbjct: 121 LAAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLT 180

Query: 181 ALKLAELAKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSI 240
           ALKLAELAKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSI
Sbjct: 181 ALKLAELAKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSI 240

Query: 241 KRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKL 300
           KRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKL
Sbjct: 241 KRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKL 300

Query: 301 GAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYY 360
           GAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYY
Sbjct: 301 GAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYY 360

Query: 361 APTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHR 420
           APTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHR
Sbjct: 361 APTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHR 420

Query: 421 VSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474
           VSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH
Sbjct: 421 VSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474


Lambda     K      H
   0.317    0.134    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: 894
Number of extensions: 28
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: 474
Length of database: 474
Length adjustment: 33
Effective length of query: 441
Effective length of database: 441
Effective search space:   194481
Effective search space used:   194481
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 15565 b1444 (medium chain aldehyde dehydrogenase (NCBI))
to HMM TIGR03374 (ydcW: 1-pyrroline dehydrogenase (EC 1.2.1.19))

# 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/TIGR03374.hmm
# target sequence database:        /tmp/gapView.4970.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03374  [M=472]
Accession:   TIGR03374
Description: ABALDH: 1-pyrroline dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
          0 1033.1   0.9          0 1032.9   0.9    1.0  1  lcl|FitnessBrowser__Keio:15565  b1444 medium chain aldehyde dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:15565  b1444 medium chain aldehyde dehydrogenase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1032.9   0.9         0         0       1     472 []       2     473 ..       2     473 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1032.9 bits;  conditional E-value: 0
                       TIGR03374   1 qdklliegklvagegekqavynpatgevileiaeasaeqvdaavraadaafaewgqttpkaraelllkladaieenaev 79 
                                     q+klli+g+lv+gegekq+vynpatg+v+leiaeasaeqvdaavraadaafaewgqttpk rae+llklad+ieen++v
  lcl|FitnessBrowser__Keio:15565   2 QHKLLINGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQV 80 
                                     79***************************************************************************** PP

                       TIGR03374  80 faklesrncgkplhavlndeipaivdvfrffagaarclsglaageyleghtsmirrdpvgvvasiapwnyplmmaawkl 158
                                     fa+lesrncgkplh+++ndeipaivdvfrffagaarcl+glaageyleghtsmirrdp+gvvasiapwnyplmmaawkl
  lcl|FitnessBrowser__Keio:15565  81 FAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKL 159
                                     ******************************************************************************* PP

                       TIGR03374 159 apalaagncvvlkpseitpltalklaelakdilpagvvnvlfgrgktvgdaltghekvrmvsltgsiatgehilahtaa 237
                                     apalaagncvvlkpseitpltalklaelakdi+pagv+n+lfgrgktvgd+ltgh+kvrmvsltgsiatgehi++hta+
  lcl|FitnessBrowser__Keio:15565 160 APALAAGNCVVLKPSEITPLTALKLAELAKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTAS 238
                                     ******************************************************************************* PP

                       TIGR03374 238 sikrthmelggkapvivfddadidavvegvrtfgfynagqdctaacriyaqrgiydelveklgkavatlkigapedest 316
                                     sikrthmelggkapvivfddadi+avvegvrtfg+ynagqdctaacriyaq+giyd+lveklg+avatlk+gap+dest
  lcl|FitnessBrowser__Keio:15565 239 SIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPDDEST 317
                                     ******************************************************************************* PP

                       TIGR03374 317 elgplsslahlervsaaveeakalshikvitggekvkgkgyyfaptllagakqddaivqkevfgpvvsitvfddeeqvv 395
                                     elgplsslahlerv +aveeaka++hikvitggek+kg+gyy+aptllaga+qddaivqkevfgpvvs+t fd+eeqvv
  lcl|FitnessBrowser__Keio:15565 318 ELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVV 396
                                     ******************************************************************************* PP

                       TIGR03374 396 rwandsryglassvwtkdvgrahrlsarlqygctwvnthfmlvsemphggqklsgygkdmslygledytvvrhimvk 472
                                     +wands+yglassvwtkdvgrahr+sarlqygctwvnthfmlvsemphggqklsgygkdmslygledytvvrh+mvk
  lcl|FitnessBrowser__Keio:15565 397 NWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473
                                     ***************************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (472 nodes)
Target sequences:                          1  (474 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.58
//
[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