GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05250 in Methylocystis bryophila S285

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_085770502.1 B1812_RS04380 ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>NCBI__GCF_002117405.1:WP_085770502.1
          Length = 293

 Score =  114 bits (285), Expect = 5e-30
 Identities = 84/278 (30%), Positives = 135/278 (48%), Gaps = 20/278 (7%)

Query: 4   DKETSTTGVAASSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKST 63
           D++  +  ++   +     +AL N+   F G+ AL    F +AAGE+ +++G NGAGKS+
Sbjct: 16  DEDAQSWSLSDDHARGGATLALTNISLSFGGIQALSEIDFSVAAGEICSIIGPNGAGKSS 75

Query: 64  LMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGRE 123
           L+ +++G+Y+ D G I LD          +  +LG+    Q L L   LS   NI +GR 
Sbjct: 76  LINVITGLYRPDWGRIQLDKNSFSRMPTERLASLGVARTFQNLALFRGLSVFDNIAVGRV 135

Query: 124 P-------RKAMGLFIDEDELNRQAAAIFAR-----MRLDMDPSTPVGELTVARQQMVEI 171
                    +  GL       +R A  I        + L    +   G L    Q+ VE+
Sbjct: 136 SATRSHWLEQVFGL--PRARADRLATEIIVEEMLVFLGLGQVRNRIAGTLPYGMQKRVEL 193

Query: 172 AKALSFDSRVLIMDEPTAAL---NNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIAD 228
           A+AL+   R+L++DEP A +     AE+ E  ++ RD    G  IV I H +  + +++D
Sbjct: 194 ARALAIRPRLLLLDEPMAGMTAGEKAEMGEFIQLTRD--RFGASIVLIEHDIGVVMELSD 251

Query: 229 RVSVMRDGKYIATVPMQETSMD-TIISMMVGRALDGEQ 265
           RV+V+  G+ IA  P  +   D  +I   +G A D EQ
Sbjct: 252 RVAVLDYGRKIADGPPSDVMNDEAVIDAYLGVAHDIEQ 289



 Score = 59.7 bits (143), Expect = 1e-13
 Identities = 55/217 (25%), Positives = 109/217 (50%), Gaps = 15/217 (6%)

Query: 287 RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAV 346
           +A+ ++ F++  GEI    G  GAG++ +   I G    + G I +    +  + P + +
Sbjct: 48  QALSEIDFSVAAGEICSIIGPNGAGKSSLINVITGLYRPDWGRIQLDKN-SFSRMPTERL 106

Query: 347 AHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQ-------RAIREAAQMYV 399
           A  +G ++   ++  L  G+ V  NIA+  +   TR  +++Q       RA R A ++ V
Sbjct: 107 A-SLG-VARTFQNLALFRGLSVFDNIAVGRVSA-TRSHWLEQVFGLPRARADRLATEIIV 163

Query: 400 RQLAIKTPSVEQQARL---LSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYK 456
            ++ +     + + R+   L  G Q+++ +A+ L     +L  DEP  G+  G K+E+ +
Sbjct: 164 EEMLVFLGLGQVRNRIAGTLPYGMQKRVELARALAIRPRLLLLDEPMAGMTAGEKAEMGE 223

Query: 457 LLDALAEQ-GKAIVMISSELPEVLRMSHRVLVMCEGR 492
            +    ++ G +IV+I  ++  V+ +S RV V+  GR
Sbjct: 224 FIQLTRDRFGASIVLIEHDIGVVMELSDRVAVLDYGR 260


Lambda     K      H
   0.320    0.135    0.372 

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: 317
Number of extensions: 16
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 520
Length of database: 293
Length adjustment: 30
Effective length of query: 490
Effective length of database: 263
Effective search space:   128870
Effective search space used:   128870
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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