Alignments for a candidate for asp-kinase in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Shewanella amazonensis SB2B

Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 6936718 Sama_0905 bifunctional aspartokinase I/homeserine dehydrogenase I (RefSeq)

Query= BRENDA::P00561
         (820 letters)



>FitnessBrowser__SB2B:6936718
          Length = 821

 Score =  886 bits (2290), Expect = 0.0
 Identities = 464/820 (56%), Positives = 577/820 (70%), Gaps = 9/820 (1%)

Query: 1   MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60
           M+V+KFGGTS+AN +RF   A I+   A+  QVA VLSAPA +TN L+ M++  ++G D 
Sbjct: 1   MKVMKFGGTSLANWQRFDMAAAIVAEAAKASQVAAVLSAPATVTNGLLDMVDVAVTGGDY 60

Query: 61  LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHV----LHGISLLGQCPD 116
              +     +F  L       Q    + Q +  +    +  KH     L G++LLG+CPD
Sbjct: 61  QAVLGRVVGVFEALFDDACQHQ----VPQCREHLFAALSAQKHAWQTRLEGVALLGECPD 116

Query: 117 SINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAA 176
            + A ++  GE++S  +M  ++ A   +   +DP    LA G  LES VDI  S  R   
Sbjct: 117 GVRAEIVVAGERLSTELMVALMNAHWLSADKLDPRALFLAHGTPLESVVDIGVSKPRFKQ 176

Query: 177 SRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCD 236
             + +  + +M GFTA ++KG  V LGRNGSDYSAAVLAACL A  CEIWTDVDGVY  D
Sbjct: 177 LPLDSKRVWVMPGFTAADDKGRTVTLGRNGSDYSAAVLAACLDASSCEIWTDVDGVYNTD 236

Query: 237 PRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIG 296
           PR V DA+LL  +SYQEAMELSYFGAKVLHP+TI PIAQF IPC IKN+ NP+APGTL+ 
Sbjct: 237 PRVVADAKLLSQLSYQEAMELSYFGAKVLHPKTIAPIAQFHIPCYIKNSFNPEAPGTLVS 296

Query: 297 ASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEY 356
            + DE  L VK IS+L+N  MF VSGPGMKGMVGMA+R   A++RA +SV LITQSS EY
Sbjct: 297 NAVDETGLQVKAISSLDNQTMFDVSGPGMKGMVGMASRTLGAIARAGVSVSLITQSSCEY 356

Query: 357 SISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKF 416
           SISFCV   D  + + A+++EF LELK  LLEPL +   LAI+S++GDGMRT +G++AKF
Sbjct: 357 SISFCVAGKDAAKVQSALEQEFELELKSELLEPLEMQSGLAIVSLIGDGMRTHKGVAAKF 416

Query: 417 FAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGV 476
           F+ALA+A++NI AIAQGSSERSIS VV        +   HQ  F+  Q ++VF++G G V
Sbjct: 417 FSALAQASVNIRAIAQGSSERSISAVVEQRKVQNAIGACHQRFFDVQQYLDVFLVGAGNV 476

Query: 477 GGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGR 536
           G  LL Q+K Q   LK +HI +RVCG+ANS+ +L +  G++L NWQ  L  ++   +LG 
Sbjct: 477 GAGLLAQVKNQAEALKEQHISIRVCGIANSRKMLLDERGIDLANWQGLLNDSETGCDLGA 536

Query: 537 LIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAA 596
           ++   KE  LLNPV+VDCTSS AVAD+Y + +  G HVVTPNKKANT  + YY  LR AA
Sbjct: 537 MLAWAKEKQLLNPVLVDCTSSAAVADRYLEVMEAGMHVVTPNKKANTRDLGYYRALREAA 596

Query: 597 EKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEA 656
            + RR+FLY+TNVGAGLPVI+NL+ LL AGD+L KF+GILSGSLS+IFGKL+EGMS SEA
Sbjct: 597 LRHRRQFLYETNVGAGLPVIDNLKKLLCAGDKLHKFNGILSGSLSFIFGKLEEGMSLSEA 656

Query: 657 TTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVA 716
           T++AR+  +TEPDPRDDLSGMDVARK+LILARE G  LEL D+ ++ VLPA F+A GDV+
Sbjct: 657 TSIARDKCFTEPDPRDDLSGMDVARKVLILAREVGMPLELEDVVVDSVLPASFDANGDVS 716

Query: 717 AFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGEN 776
            FMANL + D   A  V  AR EGKVLRYVG IDE G CRV I  V    PLF VK GEN
Sbjct: 717 TFMANLHKADTEIATMVENARSEGKVLRYVGQIDESG-CRVSIQAVGPEAPLFSVKGGEN 775

Query: 777 ALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSW 816
           ALAFYS YYQP+P VLRGYGAG DVTAAG FADLLRTL+W
Sbjct: 776 ALAFYSRYYQPIPFVLRGYGAGTDVTAAGAFADLLRTLNW 815


Lambda     K      H
   0.319    0.135    0.384 

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: 1502
Number of extensions: 47
Number of successful extensions: 5
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: 820
Length of database: 821
Length adjustment: 42
Effective length of query: 778
Effective length of database: 779
Effective search space:   606062
Effective search space used:   606062
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: 56 (26.2 bits)

Align candidate 6936718 Sama_0905 (bifunctional aspartokinase I/homeserine dehydrogenase I (RefSeq))
to HMM TIGR00657 (aspartate kinase (EC 2.7.2.4))

# 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/TIGR00657.hmm
# target sequence database:        /tmp/gapView.6940.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00657  [M=442]
Accession:   TIGR00657
Description: asp_kinases: aspartate kinase
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-126  408.3   0.0   3.2e-126  407.9   0.0    1.2  1  lcl|FitnessBrowser__SB2B:6936718  Sama_0905 bifunctional aspartoki


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6936718  Sama_0905 bifunctional aspartokinase I/homeserine dehydrogenase I (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.9   0.0  3.2e-126  3.2e-126       5     441 ..       3     460 ..       1     461 [. 0.90

  Alignments for each domain:
  == domain 1  score: 407.9 bits;  conditional E-value: 3.2e-126
                         TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee....keliekirekhleal 77 
                                       V+KFGGtS++n +r++ +a iv +++ k  qv+ V+SA+a vT+ L+++++ +  + +       +  ++e  ++ +
  lcl|FitnessBrowser__SB2B:6936718   3 VMKFGGTSLANWQRFDMAAAIVAEAA-KASQVAAVLSAPATVTNGLLDMVDVAVTGGDyqavLGRVVGVFEALFDDA 78 
                                       9******************9999998.566*********************99988876444222223344444444 PP

                         TIGR00657  78 eela.sqalkeklkallekeleevkk...............ereldlilsvGEklSaallaaaleelgvkavsllga 138
                                        + + + + +e+l a+l ++ +   +               +  +++i+  GE+lS+ l+ a++++    +++ l++
  lcl|FitnessBrowser__SB2B:6936718  79 CQHQvP-QCREHLFAALSAQKH---AwqtrlegvallgecpDGVRAEIVVAGERLSTELMVALMNAHW-LSADKLDP 150
                                       444433.233333333333333...1334677888899999************************999.99999*** PP

                         TIGR00657 139 eagiltdsefgrAkvleeikterlekl.leegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiyt 214
                                       +a  l++++ ++++v + +++ r ++l l+ + + v+ GF++a++kg+++tLGR+GSD++Aa+lAa+l+A+ +ei+t
  lcl|FitnessBrowser__SB2B:6936718 151 RALFLAHGTPLESVVDIGVSKPRFKQLpLDSKRVWVMPGFTAADDKGRTVTLGRNGSDYSAAVLAACLDASSCEIWT 227
                                       **************999999999988758888********************************************* PP

                         TIGR00657 215 DVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskseee 291
                                       DVdG+y +DPr+v +A++l ++sy+Ea+EL+++GakvLhp+t+ p++++ ip+ +k++fnpea+GTl+ +  + e  
  lcl|FitnessBrowser__SB2B:6936718 228 DVDGVYNTDPRVVADAKLLSQLSYQEAMELSYFGAKVLHPKTIAPIAQFHIPCYIKNSFNPEAPGTLVSNAVD-ETG 303
                                       ***********************************************************************88.666 PP

                         TIGR00657 292 pavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkakellk...kk 363
                                        +vka+s+ +nq++++vsg++mk  +g++++ +ga+a+a+v+v li+qss e+sisf+v  +da k +++l+   + 
  lcl|FitnessBrowser__SB2B:6936718 304 LQVKAISSLDNQTMFDVSGPGMKgmVGMASRTLGAIARAGVSVSLITQSSCEYSISFCVAGKDAAKVQSALEqefEL 380
                                       ******************************************************************99999978878 PP

                         TIGR00657 364 vkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis..sseikisvvvdekdaekavealhe 438
                                       +++ + le++e++++la+vsl+G+gm++++gvaak+f+aLa++ +ni++i+  sse++is vv+++++++a+ a h+
  lcl|FitnessBrowser__SB2B:6936718 381 ELKSELLEPLEMQSGLAIVSLIGDGMRTHKGVAAKFFSALAQASVNIRAIAqgSSERSISAVVEQRKVQNAIGACHQ 457
                                       8999************************************************************************* PP

                         TIGR00657 439 klv 441
                                       +++
  lcl|FitnessBrowser__SB2B:6936718 458 RFF 460
                                       *97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (821 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: 11.71
//
[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