GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsB in Rhizobium freirei PRF 81

Align ABC transporter permease (characterized, see rationale)
to candidate WP_004109052.1 RHSP_RS03470 sugar ABC transporter permease

Query= uniprot:A0A165KPZ4
         (293 letters)



>NCBI__GCF_000359745.1:WP_004109052.1
          Length = 301

 Score =  260 bits (664), Expect = 3e-74
 Identities = 128/274 (46%), Positives = 178/274 (64%)

Query: 12  KLVVAPAFVLGFAFIYGLMVWNGVLSLTVSRMLPNYEWAGLAQYERLWEMDRWWVALKNL 71
           K+   P  +       G  +W  V S T S++LP   + GL QY RLW   RW V+++NL
Sbjct: 20  KIASIPMILTAVVIFLGGTIWTVVYSFTNSKLLPRLSFVGLDQYYRLWAAPRWTVSIENL 79

Query: 72  GIFGVGYVGGSLLIGVVLAVLLDQKIRAEGALRTIYLYPMALSFVVTGTAWKWLLNPGLG 131
            ++G+  +  SL+IG VLA L+DQKIR E   RTI+LYP ALSF+VTG  W+WLLNP  G
Sbjct: 80  AVYGILSMIFSLVIGFVLAALMDQKIRFENTFRTIFLYPFALSFIVTGLVWQWLLNPEFG 139

Query: 132 IEKMVRDWGFPNFEFGWLVDTEMAIYCVVIAGIWQSAGFAMALFLAGLRGIDDSIIKAAQ 191
           I+ +VR  G+  F F  L    + IY V+IA +WQ  G  M L LAGLRGID+ I KAA+
Sbjct: 140 IQSVVRSLGWTTFTFDPLYTPSIVIYGVLIAALWQGTGLVMCLMLAGLRGIDEDIWKAAR 199

Query: 192 VDGASLPRIYWRIVLPALRPVFFSTLMVLSHLAIKSFDLVMALTAGGPGFATDVPATFMY 251
           VDG  + + Y  +V+P +RPVF +TL++++   +K +DLV+A T+GGPG A++VPA ++Y
Sbjct: 200 VDGIPMWKTYLFVVIPMMRPVFITTLVIIASGIVKVYDLVVAQTSGGPGIASEVPAKYVY 259

Query: 252 TMSFSRGQIGLGAASATMMLATVAALVIPYLYSE 285
              F    +G G A++TMML TVA ++IP+ Y E
Sbjct: 260 DYMFQAQNLGQGFAASTMMLLTVAIVIIPWAYLE 293


Lambda     K      H
   0.327    0.141    0.451 

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: 337
Number of extensions: 14
Number of successful extensions: 1
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: 293
Length of database: 301
Length adjustment: 26
Effective length of query: 267
Effective length of database: 275
Effective search space:    73425
Effective search space used:    73425
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.

Links

Downloads

Related tools

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