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 fused aspartate kinase/homoserine dehydrogenase 2 (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate 6939072 Sama_3170 bifunctional aspartate kinase II/homoserine dehydrogenase II (RefSeq)

Query= ecocyc::ASPKINIIHOMOSERDEHYDROGII-MONOMER
         (810 letters)



>FitnessBrowser__SB2B:6939072
          Length = 797

 Score =  561 bits (1447), Expect = e-164
 Identities = 340/802 (42%), Positives = 463/802 (57%), Gaps = 22/802 (2%)

Query: 14  LHKFGGSSLADVKCYLRVAGIMAEYSQPDDMMVVSAAGSTTNQLINWLKLSQTDRLSAHQ 73
           LHKFGGSSLAD  CY RVA I+      DD++VVSAAG TTN L   L L     L   +
Sbjct: 6   LHKFGGSSLADADCYRRVAHILLTQGHSDDLVVVSAAGKTTNFLYKLLSLRDAGELWQEE 65

Query: 74  VQQTLRRYQCDLISGLLPAEEADSLISAFVSDLERLAALLD-SGINDAVYAEVVGHGEVW 132
           +Q  L  YQ +LI  LL AE+A  L     +D  +L +LL  + +ND   + VV  GE W
Sbjct: 66  LQ-VLISYQQNLIEQLLSAEQARYLRERLSTDKAQLVSLLSLATLNDYQTSHVVSFGERW 124

Query: 133 SARLMSAVLNQQGLPAAWLDAREFLRAERAAQPQVDEGLSYPLLQQLLVQHPGKRLVVTG 192
           SARLM+A+L + G+ A+ +DA   L A+  A P + E  S   +  +L +H  +R+V+TG
Sbjct: 125 SARLMAALLRESGVAASHVDACSILVADEGAVPNIREQESREKVAAMLAEHENERIVITG 184

Query: 193 FISRNNAGETVLLGRNGSDYSATQIGALAGVSRVTIWSDVAGVYSADPRKVKDACLLPLL 252
           FI  N AGET+LLGRNGSD+SAT I +LA + RVTIW+DV GV++ADP K+ DA LL  +
Sbjct: 185 FICANPAGETLLLGRNGSDFSATLIASLADIERVTIWTDVEGVFNADPNKINDAKLLKSM 244

Query: 253 RLDEASELARLAAPVLHARTLQPVSGSEIDLQLRCSYTPDQGSTRIERVLASGTGARIVT 312
            L EA  LARL +PVLH+RTLQP+  +++ + +R SY P    T +    +S   A +VT
Sbjct: 245 SLAEADRLARLGSPVLHSRTLQPLFNTQVSMAVRSSYAPHTDFTLVAPT-SSQASAPVVT 303

Query: 313 SHDDVCLIEFQVPASQDFKLAHKEIDQILKRAQVRPLAVGVHNDRQLLQFCYTSE---VA 369
           +  +V L      A  D  LA       L  + + PLA      R  L+  YT E     
Sbjct: 304 NLSEVALFSLTTQADTDALLA------TLSASGLTPLA-SWQGSRGGLELAYTPENLKQV 356

Query: 370 DSALKILDEAGLPGELRLRQGLALVAMVGAGVTRNPLHCHRFWQQLKGQPVEFTWQSDDG 429
            + LK   EA   G++ +     LVA+V A      L+   F + L  +         D 
Sbjct: 357 SAFLKANAEAYGLGDVSISNDFGLVALVSADAV---LYRKSFARLLSREAKPLY---HDT 410

Query: 430 ISLVAVLRTGPTESLIQGLHQSVFRAEKRIGLVLFGKGNIGSRWLELFAREQSTLSARTG 489
           +SLV ++       L Q +H+      KRIG++L G GNIG  W+ LF R QS+L     
Sbjct: 411 LSLVTLVPKAQVNLLTQKVHRRCAGPRKRIGVILLGVGNIGEAWVSLFRRAQSSLCRELE 470

Query: 490 FEFVLAGVVDSRRSLLSYDGLDASRALAFFNDEAVEQDEESLFLWMRAHPYDDLVVLDVT 549
               L G+V S R+ ++  G+        F + A +     LF  +     D+LV LD++
Sbjct: 471 ARIELVGLVSSSRAYINNAGVHLENWKTEFEEYATDWQYGQLFEALSTLNCDELVALDIS 530

Query: 550 ASQQLADQYLDFASHGFHVISANKLAGASDSNKYRQIHDAFEKTGRHWLYNATVGAGLPI 609
           AS  L  QY +F + G HV+SANKLAG+     YR +         +W YNA+ GAGLP+
Sbjct: 531 ASASLTLQYPEFFARGIHVVSANKLAGSGPLPFYRDLKQQLGNRRLYWRYNASCGAGLPV 590

Query: 610 NHTVRDLIDSGDTILSISGIFSGTLSWLFLQFDGSVPFTELVDQAWQQGLTEPDPRDDLS 669
            H + DL +SGD++ ++ GIFSGTL WLF  +DG  PF++LV +A   G+TEPDPRDDLS
Sbjct: 591 QHALNDLHNSGDSVEAVGGIFSGTLCWLFEHYDGQRPFSDLVIEARGLGITEPDPRDDLS 650

Query: 670 GKDVMRKLVILAREAGYNIEPDQVRVESLVPAHCEGGSIDHFFENGDELNEQMVQRLEAA 729
           G+D+ RKL+ILARE G ++E D ++VES VP H    ++D F    DEL+  M   L AA
Sbjct: 651 GRDMQRKLLILAREIGLDLELDDIQVESPVPPHLAELTLDEFLARIDELDAPMADALAAA 710

Query: 730 REMGLVLRYVARFDANG---KARVGVEAVREDHPLASLLPCDNVFAIESRWYRDNPLVIR 786
              G VLRY+A  D  G    ARVG++ V + HP A+L P DNVF I S +Y+ NPL+IR
Sbjct: 711 AAEGKVLRYIAALDRAGGQLMARVGLQWVDKAHPYANLTPGDNVFVIRSTFYQGNPLIIR 770

Query: 787 GPGAGRDVTAGAIQSDINRLAQ 808
           GPGAGR+VTA A+QSD+ ++ +
Sbjct: 771 GPGAGREVTAAAVQSDLVQICR 792


Lambda     K      H
   0.320    0.135    0.397 

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: 1429
Number of extensions: 55
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: 810
Length of database: 797
Length adjustment: 41
Effective length of query: 769
Effective length of database: 756
Effective search space:   581364
Effective search space used:   581364
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: 55 (25.8 bits)

Align candidate 6939072 Sama_3170 (bifunctional aspartate kinase II/homoserine dehydrogenase II (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.2075.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    9.1e-68  215.2   0.0    1.3e-67  214.7   0.0    1.2  1  lcl|FitnessBrowser__SB2B:6939072  Sama_3170 bifunctional aspartate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6939072  Sama_3170 bifunctional aspartate kinase II/homoserine dehydrogenase II (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.7   0.0   1.3e-67   1.3e-67       6     401 ..       7     400 ..       4     433 .. 0.84

  Alignments for each domain:
  == domain 1  score: 214.7 bits;  conditional E-value: 1.3e-67
                         TIGR00657   6 qKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee.keliekirekhlealeela 81 
                                        KFGG+S+++++  ++va+i++ + ++  + +VVvSA +++T+ L +l +  + +e  +e+++++ + + + +e+l 
  lcl|FitnessBrowser__SB2B:6939072   7 HKFGGSSLADADCYRRVAHILLTQGHS--DDLVVVSAAGKTTNFLYKLLSLRDAGELwQEELQVLISYQQNLIEQLL 81 
                                       6********************999855..589********************9999996666666666655555555 PP

                         TIGR00657  82 sqalkeklkallekeleevkk........ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgr 150
                                       s + +  l++ l +  +++ +        + ++  ++s+GE+ Sa+l+aa+l+e g  a+s ++a + +++d+    
  lcl|FitnessBrowser__SB2B:6939072  82 SAEQARYLRERLSTDKAQLVSllslatlnDYQTSHVVSFGERWSARLMAALLRESG-VAASHVDACSILVADEGAVP 157
                                       4333333333333333333334666888899*************************.77778888888888776555 PP

                         TIGR00657 151 Akvleeikterleklleeg..iivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPr 225
                                           e++++e+++++l e      v++GFi a++ ge+ +LGR+GSD++A+l+A++ + ++v i+tDV+G++ aDP+
  lcl|FitnessBrowser__SB2B:6939072 158 NI-REQESREKVAAMLAEHenERIVITGFICANPAGETLLLGRNGSDFSATLIASLADIERVTIWTDVEGVFNADPN 233
                                       55.7999999999999887678999**************************************************** PP

                         TIGR00657 226 ivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskseeepavkalsldkn 302
                                       ++++A++l+++s +Ea  La+lG+ vLh rtl+p+ + ++ + v+s++ p+++ Tl+ ++s++ +     ++++ ++
  lcl|FitnessBrowser__SB2B:6939072 234 KINDAKLLKSMSLAEADRLARLGSPVLHSRTLQPLFNTQVSMAVRSSYAPHTDFTLVAPTSSQAS---APVVTNLSE 307
                                       ************************************************************77555...555666778 PP

                         TIGR00657 303 qalvsvsgttmkpgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkakellkkkvkeekaleevevekkl 379
                                        al+s+  + +       ++ +l+  +    +  q s   +++++   e++++  + l k+  e+  l++v++ +++
  lcl|FitnessBrowser__SB2B:6939072 308 VALFSLTTQADT----DALLATLSASGLTPLASWQGSR-GGLELAYTPENLKQVSAFL-KANAEAYGLGDVSISNDF 378
                                       899999888888....5566778888898888888777.579**************98.5688999999******** PP

                         TIGR00657 380 alvslvGagmksapgvaakife 401
                                        lv+lv+a+ + + +  a++++
  lcl|FitnessBrowser__SB2B:6939072 379 GLVALVSADAVLYRKSFARLLS 400
                                       ********99988887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (797 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: 14.45
//
[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