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.6799.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: 12.12
//
[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:

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:

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:

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:

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