GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Caldicellulosiruptor hydrothermalis 108

Align Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate WP_013402068.1 CALHY_RS00465 carbohydrate ABC transporter permease

Query= TCDB::Q72KX4
         (268 letters)



>NCBI__GCF_000166355.1:WP_013402068.1
          Length = 280

 Score =  137 bits (345), Expect = 3e-37
 Identities = 81/266 (30%), Positives = 136/266 (51%), Gaps = 7/266 (2%)

Query: 10  LLLMAGFF----LLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWEAFR--PKF 63
           LL++ G F    L P+  ++  +L +   +    + + P+PP + ++  AW   +    F
Sbjct: 15  LLVVLGLFSIGQLFPLVWLIDFSLCKSGDVYGANILKIPNPPQFINYYLAWRDGKIPQYF 74

Query: 64  QNSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQFMK 123
            NSV++ V++ LL  L   + GY   +  ++ S  +   +L G+ IP  + L+P F   +
Sbjct: 75  INSVIVNVTSVLLVVLFSLMMGYAFVRMEWKWSNKVLTYVLLGLMIPIHATLLPNFVIFR 134

Query: 124 SIGLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVILPL 183
            + +  S F L++ +V + +P    +   +   IP  L E+A IDG G F I   +ILPL
Sbjct: 135 QLKMLDSYFALIIPYVAFSLPQAVFLMTGFIGSIPRALEESAIIDGCGIFRILFQIILPL 194

Query: 184 SVPAFVVVAIWQFTQIWNEFLFAVT-LTRPESQPITVALAQLAGGEAVKWNLPMAGAILA 242
           S PA V V +  F   WNEF+ A T LT  + + +  ++   AG  A  + +  A   + 
Sbjct: 195 SKPAIVTVTVTTFLNTWNEFIMAATYLTSDKFRTLPFSVYNFAGQYASNYAVQFAVMTIV 254

Query: 243 ALPTLLVYILLGRYFLRGLLAGSVKG 268
           ALP+L+VYI L     +G+  G+VKG
Sbjct: 255 ALPSLIVYIALNEQVTKGVTLGAVKG 280


Lambda     K      H
   0.330    0.146    0.461 

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: 243
Number of extensions: 13
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 268
Length of database: 280
Length adjustment: 25
Effective length of query: 243
Effective length of database: 255
Effective search space:    61965
Effective search space used:    61965
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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