Aligments for a candidate for ilvH in Shewanella sp. ANA-3

GapMind for Amino acid biosynthesis

Aligments for a candidate for ilvH in Shewanella sp. ANA-3

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate 7025106 Shewana3_2269 acetolactate synthase 3 catalytic subunit (RefSeq)

Query= BRENDA::P00893
         (574 letters)



>FitnessBrowser__ANA3:7025106
          Length = 572

 Score =  887 bits (2291), Expect = 0.0
 Identities = 425/573 (74%), Positives = 491/573 (85%), Gaps = 2/573 (0%)

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

Query: 61  LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120
            ARATG+VGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQV ++LIG DAFQECDM+G
Sbjct: 61  YARATGKVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVPSNLIGNDAFQECDMIG 120

Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180
           ISRPVVKHSFLV+    IP+++KKAF++A++GRPGPVVVDLPKD LNPA    Y++PES+
Sbjct: 121 ISRPVVKHSFLVQDPTQIPEIIKKAFYIASTGRPGPVVVDLPKDCLNPALLHDYIYPESI 180

Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240
            MRSYNPTT+GHKGQI+R LQ L+AAKKPV+YVGGGAI + C +Q+    E LN+PVV +
Sbjct: 181 KMRSYNPTTSGHKGQIRRGLQALLAAKKPVLYVGGGAIISSCEKQILALAEKLNIPVVST 240

Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300
           LMGLGAFP TH+ +LGMLGMHG YEANMTMHN D+IF +GVRFDDRTTNN+ KYCPNAT+
Sbjct: 241 LMGLGAFPGTHKNSLGMLGMHGRYEANMTMHNCDLIFGIGVRFDDRTTNNIEKYCPNATI 300

Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWRAR 360
           LHIDIDP+SISKTV  DIPIVG A  VL+ ML LL +       + I  WWQ+I  WR R
Sbjct: 301 LHIDIDPSSISKTVRVDIPIVGSADIVLDSMLALLEESKESNDSEAINQWWQEITVWRNR 360

Query: 361 QCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGGL 420
            CL YD  S +IKPQ VIETL++LT G+AYV SDVGQHQMFAALYYPFDKPR WINSGGL
Sbjct: 361 NCLAYDKESNRIKPQQVIETLYKLTNGEAYVASDVGQHQMFAALYYPFDKPRHWINSGGL 420

Query: 421 GTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYLGM 480
           GTMGFGLPAA+GVKMA+P+ETVVCVTGDGSIQMNIQELSTALQY+ PV ++NLNNR+LGM
Sbjct: 421 GTMGFGLPAAMGVKMAMPDETVVCVTGDGSIQMNIQELSTALQYDTPVKIINLNNRFLGM 480

Query: 481 VKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNNRL 540
           VKQWQDMIYSGRHS SYM S+P+F ++AEAYGHVG+ IS P ELESK++EAL     +RL
Sbjct: 481 VKQWQDMIYSGRHSHSYMDSVPNFAKIAEAYGHVGMTISDPAELESKMAEAL--AMKDRL 538

Query: 541 VFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTER 573
           VF+D+ VD +EHVYPM IRGG M+EMWLSKTE+
Sbjct: 539 VFIDIMVDETEHVYPMLIRGGAMNEMWLSKTEK 571


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: 1083
Number of extensions: 29
Number of successful extensions: 2
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: 572
Length adjustment: 36
Effective length of query: 538
Effective length of database: 536
Effective search space:   288368
Effective search space used:   288368
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 7025106 Shewana3_2269 (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.20259.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   4.7e-278  909.1   0.4   5.5e-278  908.9   0.4    1.0  1  lcl|FitnessBrowser__ANA3:7025106  Shewana3_2269 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7025106  Shewana3_2269 acetolactate synthase 3 catalytic subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  908.9   0.4  5.5e-278  5.5e-278       1     556 [.       4     567 ..       4     568 .. 0.97

  Alignments for each domain:
  == domain 1  score: 908.9 bits;  conditional E-value: 5.5e-278
                         TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGat 76 
                                       l+ga+++v+sl +egv+++fGyPGG+vl+iydal+   ++ehilvrheqaa+h+adGyara+GkvGvvl+tsGPGat
  lcl|FitnessBrowser__ANA3:7025106   4 LSGASMIVRSLIDEGVKHIFGYPGGSVLDIYDALHlIPGIEHILVRHEQAAVHMADGYARATGKVGVVLVTSGPGAT 80 
                                       689********************************999*************************************** PP

                         TIGR00118  77 nlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPv 153
                                       n++tgiatay+ds+Plvvl+Gqv+++liG+dafqe+d++Gi++pv+khsflv+++ ++pei+k+af+iastGrPGPv
  lcl|FitnessBrowser__ANA3:7025106  81 NAITGIATAYMDSIPLVVLSGQVPSNLIGNDAFQECDMIGISRPVVKHSFLVQDPTQIPEIIKKAFYIASTGRPGPV 157
                                       ***************************************************************************** PP

                         TIGR00118 154 lvdlPkdvteaei..eleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlk 228
                                       +vdlPkd  ++++  ++ ++e++++++y+pt++ghk qi++ l+++ +akkPvl+vGgG+ii+ +++++  lae+l+
  lcl|FitnessBrowser__ANA3:7025106 158 VVDLPKDCLNPALlhDYIYPESIKMRSYNPTTSGHKGQIRRGLQALLAAKKPVLYVGGGAIISSCEKQILALAEKLN 234
                                       **********9972255666********************************************************* PP

                         TIGR00118 229 ipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeig 305
                                       ipv++tl+GlGafp +h+++lgmlGmhG++ean++++++dl++++G+rfddr+t+n++k++p+a+i+hididP++i+
  lcl|FitnessBrowser__ANA3:7025106 235 IPVVSTLMGLGAFPGTHKNSLGMLGMHGRYEANMTMHNCDLIFGIGVRFDDRTTNNIEKYCPNATILHIDIDPSSIS 311
                                       ***************************************************************************** PP

                         TIGR00118 306 knvkvdipivGdakkvleellkklkee.....ekkekeWlekieewkkeyilkldeeeesikPqkvikelskllkde 377
                                       k+v+vdipivG a  vl+ +l+ l+e      ++  ++W+++i+ w+++++l++d+e++ ikPq+vi++l+kl+++e
  lcl|FitnessBrowser__ANA3:7025106 312 KTVRVDIPIVGSADIVLDSMLALLEESkesndSEAINQWWQEITVWRNRNCLAYDKESNRIKPQQVIETLYKLTNGE 388
                                       *********************99998865542222245*************************************** PP

                         TIGR00118 378 aivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveyd 454
                                       a+v++dvGqhqm+aa +y+++kpr++i+sgGlGtmGfGlPaa+G+k+a+p+etvv+vtGdgs+qmn+qelst+ +yd
  lcl|FitnessBrowser__ANA3:7025106 389 AYVASDVGQHQMFAALYYPFDKPRHWINSGGLGTMGFGLPAAMGVKMAMPDETVVCVTGDGSIQMNIQELSTALQYD 465
                                       ***************************************************************************** PP

                         TIGR00118 455 ipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvll 530
                                       +pvki++lnn++lGmvkqWq+++y++r+s++++ s +p+f+k+aeayG++g++i++p+ele+k++eal++k ++v++
  lcl|FitnessBrowser__ANA3:7025106 466 TPVKIINLNNRFLGMVKQWQDMIYSGRHSHSYMDS-VPNFAKIAEAYGHVGMTISDPAELESKMAEALAMKdRLVFI 541
                                       **********************************5.********************************988799*** PP

                         TIGR00118 531 dvevdkeeevlPmvapGagldelvee 556
                                       d+ vd++e+v+Pm+++G++++e++ +
  lcl|FitnessBrowser__ANA3:7025106 542 DIMVDETEHVYPMLIRGGAMNEMWLS 567
                                       ***********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (572 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: 00:00:00.03
# Mc/sec: 9.94
//
[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