Alignments for a candidate for leuC in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Pedobacter sp. GW460-11-11-14-LB5

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate CA265_RS15830 CA265_RS15830 3-isopropylmalate dehydratase large subunit

Query= uniprot:A0A1X9Z7T5
         (470 letters)



>FitnessBrowser__Pedo557:CA265_RS15830
          Length = 470

 Score =  946 bits (2445), Expect = 0.0
 Identities = 470/470 (100%), Positives = 470/470 (100%)

Query: 1   MSKTLVEKIWDAHVVKSEEGFPDILYIDTHLIHEVTSPQAFDGLRKRGLPVFRPKQTVAT 60
           MSKTLVEKIWDAHVVKSEEGFPDILYIDTHLIHEVTSPQAFDGLRKRGLPVFRPKQTVAT
Sbjct: 1   MSKTLVEKIWDAHVVKSEEGFPDILYIDTHLIHEVTSPQAFDGLRKRGLPVFRPKQTVAT 60

Query: 61  ADHNVPTLNQLLPIKEELSRYQVDMLTKNCAEFGVELYGLGHPFQGIVHVIGPELGITLP 120
           ADHNVPTLNQLLPIKEELSRYQVDMLTKNCAEFGVELYGLGHPFQGIVHVIGPELGITLP
Sbjct: 61  ADHNVPTLNQLLPIKEELSRYQVDMLTKNCAEFGVELYGLGHPFQGIVHVIGPELGITLP 120

Query: 121 GKTMVCGDSHTSTHGAFGAIAFGIGTSQVEQVFATQCLLQSKPKTMKIEVNGELGKGVGA 180
           GKTMVCGDSHTSTHGAFGAIAFGIGTSQVEQVFATQCLLQSKPKTMKIEVNGELGKGVGA
Sbjct: 121 GKTMVCGDSHTSTHGAFGAIAFGIGTSQVEQVFATQCLLQSKPKTMKIEVNGELGKGVGA 180

Query: 181 KDIILYIIAKISAAGGTGYFIEYAGSAIEALSMEARMTICNMSIEMGARGGLIAPDQTTF 240
           KDIILYIIAKISAAGGTGYFIEYAGSAIEALSMEARMTICNMSIEMGARGGLIAPDQTTF
Sbjct: 181 KDIILYIIAKISAAGGTGYFIEYAGSAIEALSMEARMTICNMSIEMGARGGLIAPDQTTF 240

Query: 241 DYIKGREFAPAGEEWDKALAYWKTLYSDADAKFDSVLTFDAADIAPMITYGTNPGMGMGI 300
           DYIKGREFAPAGEEWDKALAYWKTLYSDADAKFDSVLTFDAADIAPMITYGTNPGMGMGI
Sbjct: 241 DYIKGREFAPAGEEWDKALAYWKTLYSDADAKFDSVLTFDAADIAPMITYGTNPGMGMGI 300

Query: 301 QEHIPATGAQPEKEKLSYQKALDYMGFDDDSSLIGKPVDYVFIGSCTNSRIEDLREVADF 360
           QEHIPATGAQPEKEKLSYQKALDYMGFDDDSSLIGKPVDYVFIGSCTNSRIEDLREVADF
Sbjct: 301 QEHIPATGAQPEKEKLSYQKALDYMGFDDDSSLIGKPVDYVFIGSCTNSRIEDLREVADF 360

Query: 361 VKDKRKADNVTVWIVPGSKQVEQQAKNEGLDKIFEAAGFQLREPGCSACLGMNEDKIPAG 420
           VKDKRKADNVTVWIVPGSKQVEQQAKNEGLDKIFEAAGFQLREPGCSACLGMNEDKIPAG
Sbjct: 361 VKDKRKADNVTVWIVPGSKQVEQQAKNEGLDKIFEAAGFQLREPGCSACLGMNEDKIPAG 420

Query: 421 KYCVSTSNRNFEGRQGQNARTLLASPLTAAAAAVTGKITDVRDLLDKVEG 470
           KYCVSTSNRNFEGRQGQNARTLLASPLTAAAAAVTGKITDVRDLLDKVEG
Sbjct: 421 KYCVSTSNRNFEGRQGQNARTLLASPLTAAAAAVTGKITDVRDLLDKVEG 470


Lambda     K      H
   0.317    0.135    0.399 

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: 862
Number of extensions: 13
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: 470
Length of database: 470
Length adjustment: 33
Effective length of query: 437
Effective length of database: 437
Effective search space:   190969
Effective search space used:   190969
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 CA265_RS15830 CA265_RS15830 (3-isopropylmalate dehydratase large subunit)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

# 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.aa/TIGR00170.hmm
# target sequence database:        /tmp/gapView.19203.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00170  [M=466]
Accession:   TIGR00170
Description: leuC: 3-isopropylmalate dehydratase, large subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.1e-216  705.8   0.0   1.3e-216  705.6   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS15830  CA265_RS15830 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS15830  CA265_RS15830 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  705.6   0.0  1.3e-216  1.3e-216       1     466 []       1     464 [.       1     464 [. 0.99

  Alignments for each domain:
  == domain 1  score: 705.6 bits;  conditional E-value: 1.3e-216
                                  TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhniste 68 
                                                m+ktl+ek++dahvvk +e+ +d+lyid hl+hevtspqaf+glr++g +v r+++t+at dhn++t 
  lcl|FitnessBrowser__Pedo557:CA265_RS15830   1 MSKTLVEKIWDAHVVKSEEGFPDILYIDTHLIHEVTSPQAFDGLRKRGLPVFRPKQTVATADHNVPTL 68 
                                                79****************************************************************** PP

                                  TIGR00170  69 srdveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathga 136
                                                ++ + ikee ++ qv  l+kn+ efgv+l++l +  qgivhv+gpe g+tlpgkt+vcgdsht+thga
  lcl|FitnessBrowser__Pedo557:CA265_RS15830  69 NQLLPIKEELSRYQVDMLTKNCAEFGVELYGLGHPFQGIVHVIGPELGITLPGKTMVCGDSHTSTHGA 136
                                                ******************************************************************** PP

                                  TIGR00170 137 fgalafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefa 204
                                                fga+afgigts+ve v+atq l q+++kt+kiev+g+l kg+ akdiil+ii ki++aggtgy +e+a
  lcl|FitnessBrowser__Pedo557:CA265_RS15830 137 FGAIAFGIGTSQVEQVFATQCLLQSKPKTMKIEVNGELGKGVGAKDIILYIIAKISAAGGTGYFIEYA 204
                                                ******************************************************************** PP

                                  TIGR00170 205 geairdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegak 272
                                                g ai++lsme+rmt+cnm+ie+ga+ gliapd+ttf+y+k+r++ap g+e++ka+aywktl +d +ak
  lcl|FitnessBrowser__Pedo557:CA265_RS15830 205 GSAIEALSMEARMTICNMSIEMGARGGLIAPDQTTFDYIKGREFAPAGEEWDKALAYWKTLYSDADAK 272
                                                ******************************************************************** PP

                                  TIGR00170 273 fdkvvtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvd 340
                                                fd v+t++a di+p++t+gtnpg+ + ++e++p+      + ek s +kal+y+g++ + +l    vd
  lcl|FitnessBrowser__Pedo557:CA265_RS15830 273 FDSVLTFDAADIAPMITYGTNPGMGMGIQEHIPATGA-QPEKEKLSYQKALDYMGFDDDSSLIGKPVD 339
                                                *********************************9765.5677899*********************** PP

                                  TIGR00170 341 kvfigsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagc 408
                                                 vfigsctnsriedlr+ a+ vk k++adnv  + +vpgs++v +qa++egldkif +agf+ re+gc
  lcl|FitnessBrowser__Pedo557:CA265_RS15830 340 YVFIGSCTNSRIEDLREVADFVKDKRKADNVT-VWIVPGSKQVEQQAKNEGLDKIFEAAGFQLREPGC 406
                                                *******************************9.99********************************* PP

                                  TIGR00170 409 slclgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdirel 466
                                                s clgmn+d++++++ c stsnrnfegrqg++art l sp  aaaaav+gk+ d+r+l
  lcl|FitnessBrowser__Pedo557:CA265_RS15830 407 SACLGMNEDKIPAGKYCVSTSNRNFEGRQGQNARTLLASPLTAAAAAVTGKITDVRDL 464
                                                ********************************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (470 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.19
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis