GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuG in Paraburkholderia bryophila 376MFSha3.1

Align Maltose transport system permease protein malG aka TT_C1629, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate H281DRAFT_05890 H281DRAFT_05890 carbohydrate ABC transporter membrane protein 2, CUT1 family

Query= TCDB::Q72H66
         (280 letters)



>FitnessBrowser__Burk376:H281DRAFT_05890
          Length = 317

 Score =  159 bits (403), Expect = 6e-44
 Identities = 98/309 (31%), Positives = 160/309 (51%), Gaps = 37/309 (11%)

Query: 4   ASRLLGRLFFYLLVVFVVVYSVFPFYWAVISSFKPSDALFSPDPSFLPVPFTLEHYENVF 63
           AS   G+ F   +V+   + ++ P  W  ++SFK  +   +  P  L  P ++E Y N+F
Sbjct: 12  ASSPRGKRFAAAIVITYALIAILPILWICLTSFKTQEDAIAYPPVVLFQP-SMEGYVNLF 70

Query: 64  L----------------QANFGRNL-----------------LNSLIVAGGATLLSLVLG 90
                            Q  + R++                 +NSL++  G+T L++ LG
Sbjct: 71  TIRSRQTPEFIASLPPAQTWYERDVRKRNMVIAGPSKVLPRFVNSLVIGFGSTFLAVFLG 130

Query: 91  VLAAYALGRLPFPPKNAVMYIVLSMTMFPQIAVLGGLFLLLRQTGLFNTHLGLILTYLLF 150
            LAAYA  R   P  + +++ +LS  M P IAV   ++L+ R  GL ++++G+I+ Y   
Sbjct: 131 TLAAYAFSRFKVPLADDLLFFILSTRMMPPIAVAIPIYLMYRALGLSDSYVGMIVLYTAV 190

Query: 151 TLPFTVWVLVGYFRGLPRELEEAAYVDGATPLQTLLKVMLPLTGPGLVTTGLLAFIAAWN 210
            +   VW+L G+   +PRE EEAA VDG T LQ  +KV+LP    G+  T +   I AWN
Sbjct: 191 NVSLAVWLLKGFMDEIPREYEEAALVDGYTRLQAFVKVVLPQAITGIAATAIFCLIFAWN 250

Query: 211 EYLFALTFTVGDSVKTVPPAIASFGGATPFEIPWGSIMAASVVVTVPLVVLVLVFQQRIV 270
           EY FA   T GD+ +T+PP I    G    +  W ++ AA+ +  VP+++  +V ++ ++
Sbjct: 251 EYAFASLLTSGDA-QTMPPFIPFIIGEGGQD--WPAVAAATTLFVVPILIFTVVLRKHLL 307

Query: 271 AGLTAGAVK 279
            G+T GAV+
Sbjct: 308 RGITFGAVR 316


Lambda     K      H
   0.329    0.145    0.439 

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: 176
Number of extensions: 7
Number of successful extensions: 2
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: 280
Length of database: 317
Length adjustment: 26
Effective length of query: 254
Effective length of database: 291
Effective search space:    73914
Effective search space used:    73914
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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