GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acnD in Shewanella oneidensis MR-1

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate 199538 SO0343 aconitate hydratase 1 (NCBI ptt file)

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__MR1:199538
          Length = 867

 Score = 1721 bits (4458), Expect = 0.0
 Identities = 867/867 (100%), Positives = 867/867 (100%)

Query: 1   MSTVMNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTA 60
           MSTVMNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTA
Sbjct: 1   MSTVMNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTA 60

Query: 61  SLKQIIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQL 120
           SLKQIIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQL
Sbjct: 61  SLKQIIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQL 120

Query: 121 IVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQIN 180
           IVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQIN
Sbjct: 121 IVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQIN 180

Query: 181 LERMSPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPD 240
           LERMSPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPD
Sbjct: 181 LERMSPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPD 240

Query: 241 IIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTP 300
           IIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTP
Sbjct: 241 IIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTP 300

Query: 301 EFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLS 360
           EFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLS
Sbjct: 301 EFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLS 360

Query: 361 SVVRTIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVI 420
           SVVRTIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVI
Sbjct: 361 SVVRTIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVI 420

Query: 421 AAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCN 480
           AAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCN
Sbjct: 421 AAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCN 480

Query: 481 GMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIR 540
           GMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIR
Sbjct: 481 GMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIR 540

Query: 541 FDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKV 600
           FDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKV
Sbjct: 541 FDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKV 600

Query: 601 SPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAG 660
           SPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAG
Sbjct: 601 SPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAG 660

Query: 661 EYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGI 720
           EYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGI
Sbjct: 661 EYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGI 720

Query: 721 VTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNL 780
           VTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNL
Sbjct: 721 VTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNL 780

Query: 781 VGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLD 840
           VGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLD
Sbjct: 781 VGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLD 840

Query: 841 TAEEVSIYEAGGVLQRFAQDFLESNLK 867
           TAEEVSIYEAGGVLQRFAQDFLESNLK
Sbjct: 841 TAEEVSIYEAGGVLQRFAQDFLESNLK 867


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: 2475
Number of extensions: 97
Number of successful extensions: 1
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: 867
Length adjustment: 42
Effective length of query: 825
Effective length of database: 825
Effective search space:   680625
Effective search space used:   680625
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