GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Pseudomonas simiae WCS417

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate GFF4113 PS417_21070 aconitate hydratase

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__WCS417:GFF4113
          Length = 864

 Score = 1444 bits (3738), Expect = 0.0
 Identities = 723/860 (84%), Positives = 775/860 (90%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           MNT++RKPLPG+ LDYFD R A++AI+PGAYA LPYTSRVLAENLVRRC+P  L ASL Q
Sbjct: 1   MNTEFRKPLPGSRLDYFDARAAVDAISPGAYATLPYTSRVLAENLVRRCDPATLNASLSQ 60

Query: 65  IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124
           +IE K++LDFPWFPARVVCHDILGQTALVDLAGLRDAIA +GGDPAQVNPVVPTQLIVDH
Sbjct: 61  LIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDH 120

Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184
           SLAVE GGFD DAF KNRAIEDRRNEDRFHFI WT+KAFKN+DVIP GNGIMHQINLE+M
Sbjct: 121 SLAVEAGGFDPDAFEKNRAIEDRRNEDRFHFIEWTKKAFKNVDVIPPGNGIMHQINLEKM 180

Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244
           SPVI  R+GVAFPDT VGTDSHTPHVDALGVIAIGVGGLEAESVMLGRAS+MRLP+ +GV
Sbjct: 181 SPVIQVRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPESVGV 240

Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304
           ELTGK  PGITATD+VLALTEFLR QKVV ++LEFFGEGA ALTLGDRATISNM PE+GA
Sbjct: 241 ELTGKLLPGITATDMVLALTEFLRKQKVVGAWLEFFGEGASALTLGDRATISNMAPEYGA 300

Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364
           TAAMFYIDQQT+ YL LTGRE EQV LVE YA+  GLW+DDLK A Y R L FDLSSVVR
Sbjct: 301 TAAMFYIDQQTIAYLKLTGREDEQVTLVEQYARHTGLWADDLKGAQYERGLTFDLSSVVR 360

Query: 365 TIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGL 424
            +AGPSNPHARV TS+LA++GISG+ +  PG MPDGAVIIAAITSCTNTSNPRNVIAAGL
Sbjct: 361 NMAGPSNPHARVATSDLASKGISGQWDEVPGQMPDGAVIIAAITSCTNTSNPRNVIAAGL 420

Query: 425 LARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSG 484
           LARNAN  GLTRKPWVK+SLAPGSK V +YLEEA L  ELE LGFG+V FACTTCNGMSG
Sbjct: 421 LARNANKLGLTRKPWVKSSLAPGSKTVAMYLEEAGLGHELEKLGFGVVAFACTTCNGMSG 480

Query: 485 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 544
           ALDPVIQQE+IDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE
Sbjct: 481 ALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 540

Query: 545 KDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPLY 604
           KDVLGLD +GK +RL +IWPSD EIDAV+ ASVKPEQFR VY PMF +  D G KV+PLY
Sbjct: 541 KDVLGLDANGKEIRLQDIWPSDEEIDAVVKASVKPEQFRAVYIPMFAIHEDTGPKVAPLY 600

Query: 605 DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLH 664
           DWRPQSTYIRRPPYWEGALAG R LKGMRPLAVL DNITTDHLSPSNAIM+DSAAGEYL 
Sbjct: 601 DWRPQSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIMLDSAAGEYLA 660

Query: 665 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRM 724
           KMGLPE DFNSYATHRGDHLTAQRATFANPKL NEM + +GKVKQGSLARIEPEG VTRM
Sbjct: 661 KMGLPEVDFNSYATHRGDHLTAQRATFANPKLFNEMVVENGKVKQGSLARIEPEGQVTRM 720

Query: 725 WEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMG 784
           WEAIETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAI AEGFERIHRTNLVGMG
Sbjct: 721 WEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTNLVGMG 780

Query: 785 VLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEE 844
           VLPLEF  G +R T  IDG+E +DV+G+  PRA LT++I RKNGERVEVPVTCRLDTAEE
Sbjct: 781 VLPLEFLPGTDRHTLKIDGSETYDVVGARTPRAQLTLVINRKNGERVEVPVTCRLDTAEE 840

Query: 845 VSIYEAGGVLQRFAQDFLES 864
           VSIYEAGGVLQRFAQDFLES
Sbjct: 841 VSIYEAGGVLQRFAQDFLES 860


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: 2222
Number of extensions: 92
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: 864
Length adjustment: 42
Effective length of query: 825
Effective length of database: 822
Effective search space:   678150
Effective search space used:   678150
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