GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Ss in Acidovorax sp. GW101-3H11

Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate Ac3H11_2051 Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)

Query= TCDB::Q97UG5
         (617 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2051
          Length = 348

 Score =  212 bits (540), Expect = 2e-59
 Identities = 119/326 (36%), Positives = 189/326 (57%), Gaps = 9/326 (2%)

Query: 3   EIMDSLLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLL 62
           +I  SLL+V  L   +  + G +  + +++F + P EI  + GESG GKS    AI GLL
Sbjct: 9   DIPMSLLEVKNLVVEFPGRRGTLRALDDISFSIAPGEILGVVGESGAGKSLTGAAIIGLL 68

Query: 63  KYPGVVLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAV 122
           + PG V  G + L+ + I +++ EE+R +R +    + Q  + +L+P+  +G Q+    +
Sbjct: 69  EPPGRVASGQILLEGQRIDNLSNEEMRHIRGRRIGAIFQDPLTSLNPLYTVGRQLTETIL 128

Query: 123 SH-GVNVEEARKLIKEKLELVDLPY--NVVNMYPHELSGGMRQRVVIATSILLNPSLIIL 179
           +H  V   EAR+     L+   +P     ++ YPH+ SGGMRQRVVIA ++   P LI+ 
Sbjct: 129 AHLPVTPAEARQRAIALLKDTGIPAAEERIDHYPHQFSGGMRQRVVIALALAAEPKLIVA 188

Query: 180 DEPTTGLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGS 239
           DEPTT LDV +Q +I+  LK I +  G ++++I+HD+ ++    DRV ++YAG + EIG 
Sbjct: 189 DEPTTALDVSIQAQIITLLKNICKSRGAAVMLITHDMGVIAETCDRVAVLYAGRVAEIGP 248

Query: 240 KEEIIKRPSHPYTYLLISSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEK 299
             ++I +PSHPYT  L++S+P +   RE+L  I G  P  L+ +P  C +  RCP   ++
Sbjct: 249 VHDVINKPSHPYTSGLMASIPDMTMDRERLNQIDGAMP-RLNAIPKGCAYNPRCPQTFDR 307

Query: 300 CSTLNPALGDIM--DGHKARCFLQKG 323
           C T  P   D+M     +A C+L  G
Sbjct: 308 CMTERP---DLMPAGSTRAACWLHAG 330



 Score =  166 bits (420), Expect = 1e-45
 Identities = 93/254 (36%), Positives = 146/254 (57%), Gaps = 12/254 (4%)

Query: 370 KNLILSEP-----INAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQ----TSG 420
           KNL++  P     + A++D+SF +  G I  +VG SG GKS     + G+++      SG
Sbjct: 18  KNLVVEFPGRRGTLRALDDISFSIAPGEILGVVGESGAGKSLTGAAIIGLLEPPGRVASG 77

Query: 421 KIILLGKDVSEYGVRNSMWYK-ENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKD 479
           +I+L G+ +           +   +  IFQDP +SL+P +TV   +   +L H  V+  +
Sbjct: 78  QILLEGQRIDNLSNEEMRHIRGRRIGAIFQDPLTSLNPLYTVGRQLTETILAHLPVTPAE 137

Query: 480 QLLPKIIEVLKNVGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLD 539
               + I +LK+ G+   E+ +  YPH+ SGG RQRV IA A A EPK++VADEP + LD
Sbjct: 138 AR-QRAIALLKDTGIPAAEERIDHYPHQFSGGMRQRVVIALALAAEPKLIVADEPTTALD 196

Query: 540 ASLRAGILNLIKKF-KKNGISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNP 598
            S++A I+ L+K   K  G +++ ITHD+  +    D + V+Y GR+ E G  ++VI+ P
Sbjct: 197 VSIQAQIITLLKNICKSRGAAVMLITHDMGVIAETCDRVAVLYAGRVAEIGPVHDVINKP 256

Query: 599 SHEYTKRLIEAVPD 612
           SH YT  L+ ++PD
Sbjct: 257 SHPYTSGLMASIPD 270


Lambda     K      H
   0.319    0.138    0.391 

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: 474
Number of extensions: 23
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 617
Length of database: 348
Length adjustment: 33
Effective length of query: 584
Effective length of database: 315
Effective search space:   183960
Effective search space used:   183960
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 (21.7 bits)
S2: 51 (24.3 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