GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34245 in Collimonas arenae Ter10

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate WP_061532689.1 CAter10_RS05910 sugar ABC transporter ATP-binding protein

Query= uniprot:B2T9V9
         (510 letters)



>NCBI__GCF_001584165.1:WP_061532689.1
          Length = 518

 Score =  280 bits (715), Expect = 1e-79
 Identities = 175/481 (36%), Positives = 271/481 (56%), Gaps = 17/481 (3%)

Query: 20  VTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAP 79
           VTKRF    AL++    ++ GE HAL+G NGAGKSTL+ +L+G+   D+GE+R  G    
Sbjct: 25  VTKRFPGVLALDNCQFNLLRGEVHALMGENGAGKSTLMKVLSGVYPKDSGEIRMDGRPVE 84

Query: 80  SIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPL-RGGV-IDWQAMRRDARALLDH 137
               R A    +  ++Q   ++  LS A+N+FI R+P  R GV +D  A+ R A  + + 
Sbjct: 85  IPNPRAAQALGIGIIHQELNLMNHLSAAQNIFIGREPRGRYGVFLDEDALNRQAAQIFER 144

Query: 138 WKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQ 197
            ++ +      G+L+V  +Q+VEIA+ALS+ +R +I+DEPTA L+  EI  LFR I +LQ
Sbjct: 145 MRLQLDPRTLVGELTVAKQQMVEIAKALSFDSRVLIMDEPTAALNNAEIDDLFRIIRQLQ 204

Query: 198 REGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTG---ERGGLA 254
             GV  ++ISH + E+ +I   VTV+RD ++I + P    P + +I  M G   +  G  
Sbjct: 205 EHGVGIIYISHKMDELRQISNRVTVMRDGQYIATVPTVGTPIDTIIGMMVGRQLDNSGPE 264

Query: 255 VADAAARGALPADTAVALELKELT-GADYEGVSFTVKRGEVVGLTGATSSGRTSVAEAIA 313
           V D +A         V LE+K LT GA  + V+F++++GE++G  G   +GRT VA A+ 
Sbjct: 265 VPDTSAND-------VVLEVKGLTRGAAIKDVNFSLRKGEILGFAGLMGAGRTEVARAVF 317

Query: 314 GLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASM-TIARV 372
           G  A   G I V G  +       ++AHGIG + +DR H GL     V  N  M ++ + 
Sbjct: 318 GADAIDAGEILVHGVKVSIKSPRDAVAHGIGYLSEDRKHFGLATGLDVKTNVVMSSMDKF 377

Query: 373 LGK-FGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLV 431
           L K   +  PA +    Q  +  L I     +  V  LSGGNQQK+V+A+ L  + ++L 
Sbjct: 378 LTKGLFLDQPAIRET-AQGYVRQLSIKTPSIDQPVRLLSGGNQQKIVIAKWLLRDCDILF 436

Query: 432 LIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGRVAAEFP 490
             +PT G+D+ +K  +  +++ +  +GKA++++S EL + LR   R+LVM  GR+  E  
Sbjct: 437 FDEPTRGIDIGAKNEIYKLLNALAAQGKAIVMISSELPEVLRMSHRILVMCEGRITGELA 496

Query: 491 A 491
           A
Sbjct: 497 A 497


Lambda     K      H
   0.318    0.134    0.377 

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: 546
Number of extensions: 28
Number of successful extensions: 9
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: 510
Length of database: 518
Length adjustment: 35
Effective length of query: 475
Effective length of database: 483
Effective search space:   229425
Effective search space used:   229425
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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