Alignments for a candidate for hcs in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for hcs in Klebsiella michiganensis M5al

Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate BWI76_RS18860 BWI76_RS18860 homocitrate synthase

Query= BRENDA::A0A1Y6KBA1
         (416 letters)



>FitnessBrowser__Koxy:BWI76_RS18860
          Length = 380

 Score =  307 bits (787), Expect = 3e-88
 Identities = 171/371 (46%), Positives = 229/371 (61%)

Query: 38  MPRVILNDTTLRDGEQAPGVAFALSEKVAIARALARAGVPEIEAGTPAMGADEISAIRAI 97
           M RV++NDTTLRDGEQ+PGVAF  SEKVAIA AL  AG+  +E GTPAMG +EI+ I+ +
Sbjct: 1   MERVLINDTTLRDGEQSPGVAFRTSEKVAIAEALYAAGITAMEVGTPAMGDEEIARIQLV 60

Query: 98  VEAGLPATIIGWCRMREADVDAAIAAGVSMVNVSIPTSDVQIAAKLGGGRSVALELLKRV 157
                 AT++ WCRM   ++  +   G+  V++SIP SD     KL    +V LE L   
Sbjct: 61  RRQLPDATLMTWCRMNALEIRQSADLGIDWVDISIPASDKLRQYKLREPLAVLLERLAMF 120

Query: 158 VSYARSRGLGVAVGGEDSSRADVGFLAEVIATAKALGARRFRVADTLSVLDPDATSALVG 217
           +  A + GL V +G ED+SRA    L  +   A+   A R R ADT+ +LDP  T+A + 
Sbjct: 121 IHLAHTLGLKVCIGCEDASRASGQTLRAIAEVAQQCAAARLRYADTVGLLDPFTTAAQIS 180

Query: 218 ALRATTDLEIEFHGHDDLGLATANTLAAIKAGATHASVTVIGLGERAGNAPLEEVAVALR 277
           ALR     EIE H H+DLG+ATANTLAA+ AGAT  + TV+GLGERAGNA LE VA+ L 
Sbjct: 181 ALRDVWSGEIEMHAHNDLGMATANTLAAVSAGATSVNTTVLGLGERAGNAALETVALGLE 240

Query: 278 QLYRRETGIVLAELDHVANVVAAAAARAIPLNKAIVGEHVFTHESGIHVDGLLKDQRTYQ 337
           +    ETG+  + L  +   VA AA RAI   + +VGE VFTHESG+HV  LL+D  +YQ
Sbjct: 241 RCLGVETGVHFSALPALCQRVAEAAQRAIDPQQPLVGELVFTHESGVHVAALLRDSESYQ 300

Query: 338 ALDPMLFGRSNRIVIGKHSGLSAITSLLSDLRLPASADQAQRILARVRKHAVAHKGPVPK 397
           ++ P L GRS R+V+GKHSG  A+  +   +    +A Q  ++L  +R+ A   K     
Sbjct: 301 SIAPSLMGRSYRLVLGKHSGRQAVNGVFDQMGYHLNAAQINQLLPAIRRFAENWKRSPKD 360

Query: 398 EAVAAIWREVC 408
             + AI+ E+C
Sbjct: 361 YELVAIYDELC 371


Lambda     K      H
   0.317    0.132    0.369 

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: 358
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: 416
Length of database: 380
Length adjustment: 31
Effective length of query: 385
Effective length of database: 349
Effective search space:   134365
Effective search space used:   134365
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: 50 (23.9 bits)

Align candidate BWI76_RS18860 BWI76_RS18860 (homocitrate synthase)
to HMM TIGR02660 (nifV: homocitrate synthase (EC 2.3.3.14))

# 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/TIGR02660.hmm
# target sequence database:        /tmp/gapView.8535.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02660  [M=365]
Accession:   TIGR02660
Description: nifV_homocitr: homocitrate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
     4e-168  545.3   1.1   4.5e-168  545.1   1.1    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS18860  BWI76_RS18860 homocitrate syntha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS18860  BWI76_RS18860 homocitrate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  545.1   1.1  4.5e-168  4.5e-168       2     365 .]       4     367 ..       3     367 .. 1.00

  Alignments for each domain:
  == domain 1  score: 545.1 bits;  conditional E-value: 4.5e-168
                               TIGR02660   2 vlinDttLRDGEqaagvaFsaeEKlaiAkaLdeaGvdelEvGipamgeeEraairaiaalglkarllaWcR 72 
                                             vlinDttLRDGEq++gvaF+++EK+aiA+aL++aG++ +EvG+pamg+eE+a+i+ ++++ ++a+l++WcR
  lcl|FitnessBrowser__Koxy:BWI76_RS18860   4 VLINDTTLRDGEQSPGVAFRTSEKVAIAEALYAAGITAMEVGTPAMGDEEIARIQLVRRQLPDATLMTWCR 74 
                                             89********************************************************************* PP

                               TIGR02660  73 lraedieaaaevGvkavdlsvpvsdlqleaklkkdrawvleelkelvslakeeglkvsvgaeDasRadeef 143
                                             ++a +i+++a++G+++vd+s+p+sd+ +++kl++  a++le+l+++++la++ glkv++g+eDasRa+ ++
  lcl|FitnessBrowser__Koxy:BWI76_RS18860  75 MNALEIRQSADLGIDWVDISIPASDKLRQYKLREPLAVLLERLAMFIHLAHTLGLKVCIGCEDASRASGQT 145
                                             *********************************************************************** PP

                               TIGR02660 144 lvelaevakeagakRlRfaDtvgvldPfstyelvkalraalelelElHaHnDlGlAtAntlaavkaGassv 214
                                             l+++aeva++  a+RlR+aDtvg+ldPf+t+++++alr+ ++ e+E+HaHnDlG+AtAntlaav+aGa+sv
  lcl|FitnessBrowser__Koxy:BWI76_RS18860 146 LRAIAEVAQQCAAARLRYADTVGLLDPFTTAAQISALRDVWSGEIEMHAHNDLGMATANTLAAVSAGATSV 216
                                             *********************************************************************** PP

                               TIGR02660 215 svtvlGlGERAGnAaleevalalkellgldtgidlselkelsqlvakasgraleaqkavvGesvFaHEsGi 285
                                             ++tvlGlGERAGnAale val+l+++lg++tg+++s+l++l+q va+a++ra+++q+++vGe vF+HEsG+
  lcl|FitnessBrowser__Koxy:BWI76_RS18860 217 NTTVLGLGERAGNAALETVALGLERCLGVETGVHFSALPALCQRVAEAAQRAIDPQQPLVGELVFTHESGV 287
                                             *********************************************************************** PP

                               TIGR02660 286 HvdgllkdeatYesldPeevGrerelviGKHsgraaviealkelgleleeeeaeelleavravaerlKrsl 356
                                             Hv++ll+d+++Y+s++P+++Gr+++lv+GKHsgr+av+ +++++g++l+++++++ll+a+r++ae++Krs+
  lcl|FitnessBrowser__Koxy:BWI76_RS18860 288 HVAALLRDSESYQSIAPSLMGRSYRLVLGKHSGRQAVNGVFDQMGYHLNAAQINQLLPAIRRFAENWKRSP 358
                                             *********************************************************************** PP

                               TIGR02660 357 eeeelaalv 365
                                             ++ el+a++
  lcl|FitnessBrowser__Koxy:BWI76_RS18860 359 KDYELVAIY 367
                                             *****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (380 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: 00:00:00.01
# Mc/sec: 10.15
//
[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