Aligments for a candidate for ilvH in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Aligments for a candidate for ilvH in Shewanella amazonensis SB2B

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate 6937877 Sama_2018 acetolactate synthase 3 catalytic subunit (RefSeq)

Query= BRENDA::P00893
         (574 letters)



>FitnessBrowser__SB2B:6937877
          Length = 573

 Score =  895 bits (2312), Expect = 0.0
 Identities = 434/575 (75%), Positives = 498/575 (86%), Gaps = 3/575 (0%)

Query: 1   MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG 60
           ME LSGA M+VRSLID+GVK +FGYPGG+VLDIYDALH    I+H+LVRHEQAAVHMADG
Sbjct: 1   MEKLSGASMIVRSLIDEGVKHIFGYPGGSVLDIYDALHESSNIEHILVRHEQAAVHMADG 60

Query: 61  LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120
            ARATG+VGVVLVTSGPGATNAITGIATAYMDS+PLV+LSGQV +SLIG DAFQECDM+G
Sbjct: 61  YARATGDVGVVLVTSGPGATNAITGIATAYMDSVPLVILSGQVPSSLIGNDAFQECDMIG 120

Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180
           ISRP+VKHSFLVK   +IP+ +KKAF++AA+GRPGPVVVDLPKD LNPA K  Y +P  V
Sbjct: 121 ISRPIVKHSFLVKDPTEIPETIKKAFYIAATGRPGPVVVDLPKDTLNPALKFDYEYPSEV 180

Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240
            MRSYNPT TGHKGQI+R LQ L+ AKKPV+YVGGGAI + C +Q+    E LN+PVV +
Sbjct: 181 KMRSYNPTVTGHKGQIRRGLQALLNAKKPVLYVGGGAIISSCDKQILALSERLNIPVVNT 240

Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300
           LMGLGAFP TH   +GMLGMHGTYEANMTMHN+D+IF +GVRFDDRTTNN+ KYCPNATV
Sbjct: 241 LMGLGAFPGTHPNNIGMLGMHGTYEANMTMHNSDLIFGIGVRFDDRTTNNVQKYCPNATV 300

Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRD-WWQQIEQWRA 359
           LHIDIDP+SISKTV A IPIVG A +VL++ML LL  ++  +  +   D WW  I QWR+
Sbjct: 301 LHIDIDPSSISKTVQAHIPIVGSADKVLDEMLSLLDGDTEMRNDEGAIDCWWNDINQWRS 360

Query: 360 RQCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGG 419
           R+CL Y+T+SEKIKPQ VIETL+RLTKGDAYV+SDVGQHQMFAALYYPFDKPRRWINSGG
Sbjct: 361 RKCLAYETNSEKIKPQQVIETLYRLTKGDAYVSSDVGQHQMFAALYYPFDKPRRWINSGG 420

Query: 420 LGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYLG 479
           LGTMGFGLPAA+GVKMA+P+ETVVCVTGDGSIQMNIQELSTALQY++PV ++NLNNR+LG
Sbjct: 421 LGTMGFGLPAAMGVKMAMPDETVVCVTGDGSIQMNIQELSTALQYDVPVKIINLNNRFLG 480

Query: 480 MVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNNR 539
           MVKQWQDMIYSGRHS SYM S+PDF ++AEAYGHVGI IS P ELE KL+EAL     +R
Sbjct: 481 MVKQWQDMIYSGRHSHSYMDSVPDFAKIAEAYGHVGITISRPEELEPKLAEALSM--TDR 538

Query: 540 LVFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTERT 574
           LVFVD+ VD +EHVYPMQIRGG M++MWLSKTER+
Sbjct: 539 LVFVDINVDETEHVYPMQIRGGAMNDMWLSKTERS 573


Lambda     K      H
   0.319    0.135    0.403 

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: 1086
Number of extensions: 37
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: 574
Length of database: 573
Length adjustment: 36
Effective length of query: 538
Effective length of database: 537
Effective search space:   288906
Effective search space used:   288906
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 (21.8 bits)
S2: 53 (25.0 bits)

Align candidate 6937877 Sama_2018 (acetolactate synthase 3 catalytic subunit (RefSeq))
to HMM TIGR00118 (ilvB: acetolactate synthase, large subunit, biosynthetic type (EC 2.2.1.6))

# 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/TIGR00118.hmm
# target sequence database:        /tmp/gapView.30388.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00118  [M=557]
Accession:   TIGR00118
Description: acolac_lg: acetolactate synthase, large subunit, biosynthetic type
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.4e-280  916.7   0.2   2.7e-280  916.5   0.2    1.0  1  lcl|FitnessBrowser__SB2B:6937877  Sama_2018 acetolactate synthase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937877  Sama_2018 acetolactate synthase 3 catalytic subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  916.5   0.2  2.7e-280  2.7e-280       1     556 [.       4     568 ..       4     569 .. 0.97

  Alignments for each domain:
  == domain 1  score: 916.5 bits;  conditional E-value: 2.7e-280
                         TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGat 76 
                                       l+ga+++v+sl +egv+++fGyPGG+vl+iydal+ +s++ehilvrheqaa+h+adGyara+G vGvvl+tsGPGat
  lcl|FitnessBrowser__SB2B:6937877   4 LSGASMIVRSLIDEGVKHIFGYPGGSVLDIYDALHeSSNIEHILVRHEQAAVHMADGYARATGDVGVVLVTSGPGAT 80 
                                       689********************************999*************************************** PP

                         TIGR00118  77 nlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPv 153
                                       n++tgiatay+dsvPlv+l+Gqv++sliG+dafqe+d++Gi++p++khsflvk++ ++pe++k+af+ia+tGrPGPv
  lcl|FitnessBrowser__SB2B:6937877  81 NAITGIATAYMDSVPLVILSGQVPSSLIGNDAFQECDMIGISRPIVKHSFLVKDPTEIPETIKKAFYIAATGRPGPV 157
                                       ***************************************************************************** PP

                         TIGR00118 154 lvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlk 228
                                       +vdlPkd+ ++++++++e  ++v++++y+ptv+ghk qi++ l+++ +akkPvl+vGgG+ii+ +++++  l+erl+
  lcl|FitnessBrowser__SB2B:6937877 158 VVDLPKDTLNPALKFDYEypSEVKMRSYNPTVTGHKGQIRRGLQALLNAKKPVLYVGGGAIISSCDKQILALSERLN 234
                                       **********9988877766********************************************************* PP

                         TIGR00118 229 ipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeig 305
                                       ipv+ tl+GlGafp +hp+ +gmlGmhGt+ean++++++dl++++G+rfddr+t+n++k++p+a+++hididP++i+
  lcl|FitnessBrowser__SB2B:6937877 235 IPVVNTLMGLGAFPGTHPNNIGMLGMHGTYEANMTMHNSDLIFGIGVRFDDRTTNNVQKYCPNATVLHIDIDPSSIS 311
                                       ***************************************************************************** PP

                         TIGR00118 306 knvkvdipivGdakkvleellkklkee.....ekkeke.WlekieewkkeyilkldeeeesikPqkvikelskllkd 376
                                       k+v+++ipivG a kvl+e+l+ l        ++  ++ W++ i++w+++++l++++++e+ikPq+vi++l++l+k+
  lcl|FitnessBrowser__SB2B:6937877 312 KTVQAHIPIVGSADKVLDEMLSLLDGDtemrnDEGAIDcWWNDINQWRSRKCLAYETNSEKIKPQQVIETLYRLTKG 388
                                       *********************998765555433333458************************************** PP

                         TIGR00118 377 eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstivey 453
                                       +a+v++dvGqhqm+aa +y+++kpr++i+sgGlGtmGfGlPaa+G+k+a+p+etvv+vtGdgs+qmn+qelst+ +y
  lcl|FitnessBrowser__SB2B:6937877 389 DAYVSSDVGQHQMFAALYYPFDKPRRWINSGGLGTMGFGLPAAMGVKMAMPDETVVCVTGDGSIQMNIQELSTALQY 465
                                       ***************************************************************************** PP

                         TIGR00118 454 dipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvl 529
                                       d+pvki++lnn++lGmvkqWq+++y++r+s++++ s +pdf+k+aeayG++gi+i++peele kl+eal+++ ++v+
  lcl|FitnessBrowser__SB2B:6937877 466 DVPVKIINLNNRFLGMVKQWQDMIYSGRHSHSYMDS-VPDFAKIAEAYGHVGITISRPEELEPKLAEALSMTdRLVF 541
                                       ***********************************5.********************************987699** PP

                         TIGR00118 530 ldvevdkeeevlPmvapGagldelvee 556
                                       +d++vd++e+v+Pm+++G+++++++ +
  lcl|FitnessBrowser__SB2B:6937877 542 VDINVDETEHVYPMQIRGGAMNDMWLS 568
                                       ************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (573 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: 11.65
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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, or view the source code, or see 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