GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acnD in Dechlorosoma suillum PS

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate Dsui_2347 Dsui_2347 aconitate hydratase 1

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__PS:Dsui_2347
          Length = 898

 Score =  698 bits (1801), Expect = 0.0
 Identities = 389/876 (44%), Positives = 533/876 (60%), Gaps = 50/876 (5%)

Query: 21  FDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLT-------ASLKQIIESKQELD 73
           F +  A+EA   G  ++LP + R++ E L+R C+   +T       A+ +   E  +E+ 
Sbjct: 22  FHSLPALEAAGIGPVSRLPVSLRIVLEALLRHCDGRRVTPRHVLQLANWQPRAERTEEI- 80

Query: 74  FPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAV-EYGG 132
            P+  ARVV  D  G   L DLA +RDA AA+G DP ++ P+VP  L+VDHS+ V EYG 
Sbjct: 81  -PFVVARVVLQDFTGVPLLCDLAAMRDAAAAQGTDPKRIEPLVPVDLVVDHSVQVDEYG- 138

Query: 133 FDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARN 192
               A  +N  +E +RN +R+ F+ W  +AF    V+P G GI+HQ+NLE +   +  + 
Sbjct: 139 -TPTALRRNMELEFQRNAERYQFMKWGMQAFDTFKVVPPGIGIVHQVNLEYLFRGVRRQG 197

Query: 193 GVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQP 252
            + FPDTLVGTDSHT  ++ +GV+  GVGG+EAE+ MLG+  Y   PD++GVEL G+   
Sbjct: 198 ELLFPDTLVGTDSHTTMINGVGVVGWGVGGIEAEAAMLGQPVYFLTPDVVGVELRGRLNE 257

Query: 253 GITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYID 312
           G+TATD+VL +TE LR +KVV  ++EFFG G+ +L+L DRATI+NM PE+GAT   F +D
Sbjct: 258 GVTATDLVLTVTELLRREKVVGKFVEFFGPGSTSLSLTDRATIANMAPEYGATLGFFPVD 317

Query: 313 QQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAV-YPRTLHFDLSSVVRTIAGPSN 371
           ++T+DYL  TGR   +V+  E Y +  GL+       + Y   L  DL+++V ++AGP  
Sbjct: 318 EKTVDYLRQTGRNEAEVEAFEAYFRAQGLFGAPRAGDIDYSTQLSLDLATIVPSLAGPKR 377

Query: 372 PHARVPTSEL------------AARGISGEVENEPGLMP---------DGAVIIAAITSC 410
           P  R+  S++            +A G     E  P   P          G V+IAAITSC
Sbjct: 378 PQDRIDLSDMGRSFDTLFSQPTSANGFGKPAEQLPQRQPTARAGVDLGHGDVLIAAITSC 437

Query: 411 TNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFG 470
           TNTSNP  +IAAGLLA+ A  KGL+ +P +KTSLAPGS+ V  YLE+A LL  L  LGF 
Sbjct: 438 TNTSNPAVLIAAGLLAKKAVDKGLSVQPHIKTSLAPGSRVVTDYLEKAGLLAPLARLGFA 497

Query: 471 IVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLV 530
           + G+ CTTC G +G L P   Q + +RDL   AVLSGNRNF+ RIHP  +  +LASPPLV
Sbjct: 498 LAGYGCTTCIGNAGDLAPEFNQAIAERDLVVAAVLSGNRNFEARIHPAIRANYLASPPLV 557

Query: 531 VAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMF 590
           VA+AIAG +  D+    LG  +DG+PV L  IWPS  EI  V+  +  P  +R++Y   F
Sbjct: 558 VAFAIAGRVNVDLTTTPLGTGRDGQPVYLREIWPSSEEIATVLPFAQDPATYRRLYAD-F 616

Query: 591 DLSVDYGDKV----SPLYDWRPQSTYIRRPPYWEGALAGERTL---KGMRPLAVLGDNIT 643
               D  + V      +YDW P STYI RPP+++G       L    G R L VLGD++T
Sbjct: 617 TRDHDLWNAVPAPEGQIYDW-PPSTYIARPPFFDGFTVEPPPLAPINGARALLVLGDSVT 675

Query: 644 TDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEM--A 701
           TDH+SP+ +    + AG++L   G+   DFNSY + RG H    R TFAN ++KN M   
Sbjct: 676 TDHISPAGSFKAATPAGQWLTAQGVKSLDFNSYGSRRGHHEVMVRGTFANVRVKNLMLPP 735

Query: 702 IVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRL 761
             DG   +G    ++ + +   ++EA   Y  R  P ++ AG +YG GSSRDWAAKG RL
Sbjct: 736 KADGSPVEGGYTLLDGQQVT--VFEAASAYQQRGIPTLVFAGEEYGTGSSRDWAAKGTRL 793

Query: 762 AGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAP---RAD 818
            GV A+VA  FERIHR NLVGMGVLPL+FKAG + A+ G+DG+E FD+ G+  P   + D
Sbjct: 794 LGVRAVVARSFERIHRANLVGMGVLPLQFKAGTSAASLGLDGSEHFDLPGADGPLQAQQD 853

Query: 819 LTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVL 854
           L + ITR +G   +VP+ CR+DT  EV  +  GG+L
Sbjct: 854 LMLRITRSDGRVEQVPLLCRIDTPIEVEYFRHGGIL 889


Lambda     K      H
   0.318    0.136    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: 2037
Number of extensions: 119
Number of successful extensions: 9
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: 867
Length of database: 898
Length adjustment: 43
Effective length of query: 824
Effective length of database: 855
Effective search space:   704520
Effective search space used:   704520
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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:

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