GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Klebsiella michiganensis M5al

Align High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate BWI76_RS26340 BWI76_RS26340 branched-chain amino acid ABC transporter permease

Query= TCDB::P21628
         (417 letters)



>FitnessBrowser__Koxy:BWI76_RS26340
          Length = 426

 Score =  481 bits (1239), Expect = e-140
 Identities = 256/417 (61%), Positives = 315/417 (75%), Gaps = 17/417 (4%)

Query: 8   ALFSALLVILVSYPILGLKLRTVGIKLEV-LGADAQTLWTIAAAALAMFVWQLFRDRIPL 66
           AL SA++  +++   +G++L   G KL V   AD +  W     A+  F +QL R     
Sbjct: 9   ALLSAVMFFILAGVFMGVQLELDGTKLVVDTAADIRWQWIYIGTAVVFF-FQLLRPVFQK 67

Query: 67  KLGRGVGYK-----VNGSGLKNFLSLPSTQRWAVLALVVVAFVWPFFASRGAVDIATLIL 121
            +    G K     ++GS +K        Q+  ++AL+V+A  WPF  SRG VDIATL +
Sbjct: 68  TIKNVSGPKFILPAIDGSTVK--------QKLFLIALLVIAVAWPFMVSRGTVDIATLTM 119

Query: 122 IYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAALFG 181
           IY++LG+GLN+VVGL+GLL LGY GFYA+GAYT+ALL  Y G GFWT LP+AG+++A  G
Sbjct: 120 IYIILGLGLNVVVGLSGLLVLGYGGFYAIGAYTFALLNHYYGLGFWTCLPLAGLVSAAAG 179

Query: 182 FLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFERRA 241
           FLLGFPVLRLRGDYLAIVTLGFGEI+RILL N TEITGGPNGI  IPKPTLFGL F R A
Sbjct: 180 FLLGFPVLRLRGDYLAIVTLGFGEIVRILLLNNTEITGGPNGISQIPKPTLFGLEFSRSA 239

Query: 242 PE-GMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEV 300
            E G  TF  FFG+ Y+ + +VI LY+VALLLV+L+LFVINRL+RMP+GRAWEALREDE+
Sbjct: 240 REGGWDTFSNFFGVKYDPSDRVIFLYLVALLLVVLSLFVINRLLRMPLGRAWEALREDEI 299

Query: 301 ACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGM 360
           ACR+LGL+PT +KL+AFTI A+FAGFAG+ FAARQG V+PESFTF ESA +LAIVVLGGM
Sbjct: 300 ACRSLGLSPTRIKLTAFTISAAFAGFAGTLFAARQGFVSPESFTFAESAFVLAIVVLGGM 359

Query: 361 GSQLGVILAAVVMVLLQE-MRGFNEYRMLIFGLTMIVMMIWRPQGLLPMQRPHLELK 416
           GSQ  VILAAV++V+ +E MR FNEY ML+ G  M++MMIWRPQGLLPM RP L+LK
Sbjct: 360 GSQFAVILAAVLLVVSRELMRDFNEYSMLMLGALMVLMMIWRPQGLLPMTRPQLKLK 416


Lambda     K      H
   0.330    0.146    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: 561
Number of extensions: 28
Number of successful extensions: 3
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: 417
Length of database: 426
Length adjustment: 32
Effective length of query: 385
Effective length of database: 394
Effective search space:   151690
Effective search space used:   151690
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 50 (23.9 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