GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00885 in Rhodobacter maris JA276

Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate WP_097070282.1 CRO22_RS11435 branched-chain amino acid ABC transporter permease

Query= uniprot:D8IUY4
         (309 letters)



>NCBI__GCF_900217815.1:WP_097070282.1
          Length = 289

 Score =  146 bits (369), Expect = 5e-40
 Identities = 91/303 (30%), Positives = 162/303 (53%), Gaps = 24/303 (7%)

Query: 6   QQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQVAPGLP 65
           Q I+NGL LG+ YALIALG T+++ ++N++NFAHG + ++G  +  ++  V Q   P + 
Sbjct: 3   QIIVNGLFLGASYALIALGLTLIFSLMNVLNFAHGQMYVLGGFITYTV--VAQFHLPFVV 60

Query: 66  GIVQLVIAIVGAIPVCIVVSLLIERIAYRPL--RNAPRLAPLITAIGVSILLQTLAMMIW 123
           G++   +A+         +    ER  + P+  R+    + ++ A G++  L  + ++++
Sbjct: 61  GLICSAVALA-------ALGAFAERFLFAPVIRRSKREESTMLLAAGIAFFLDAVTLLVF 113

Query: 124 GRSPLPFPQVMPSDPVHIAGALISPTQIMLLALAVLAMVGLVLIVEKTKMGRAMRATAEN 183
           G      P+++          ++   +I++  LAV  +   +L +  ++ GRAMRA A++
Sbjct: 114 GEKQRGIPKIVQGVFNWDFRIVMPYDRILIGCLAVALIAAFILFMRLSRTGRAMRALAQD 173

Query: 184 PRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKAFSAAVLGG 243
              A LMGVD  +  ++ FA+GA LA + G +   +       MG    +KAF   ++GG
Sbjct: 174 RMAAELMGVDVGRYSMIGFALGAMLAGLVGGL-LVSIVGVNLGMGGPTSIKAFMMIMIGG 232

Query: 244 IGNIYGAMLGGILLGLIESLGAGYI---GDLTGNFLGSNYQDIFAFIVLIIVLTLRPSGI 300
            G I GA+ GG +LG++ES+G   +   GD+T          +  F+ L+I L  RP G+
Sbjct: 233 AGVISGAIAGGFILGMLESVGLSLLAAYGDIT---------YLVIFVSLLIFLAFRPQGL 283

Query: 301 MGE 303
           MG+
Sbjct: 284 MGK 286


Lambda     K      H
   0.328    0.144    0.416 

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: 255
Number of extensions: 19
Number of successful extensions: 4
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: 309
Length of database: 289
Length adjustment: 27
Effective length of query: 282
Effective length of database: 262
Effective search space:    73884
Effective search space used:    73884
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 (21.7 bits)
S2: 48 (23.1 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