GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Caldicellulosiruptor hydrothermalis 108

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_013402438.1 CALHY_RS02475 sugar ABC transporter ATP-binding protein

Query= uniprot:G8ALJ0
         (294 letters)



>NCBI__GCF_000166355.1:WP_013402438.1
          Length = 499

 Score = 99.4 bits (246), Expect = 2e-25
 Identities = 81/275 (29%), Positives = 136/275 (49%), Gaps = 21/275 (7%)

Query: 4   QSMTTTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTP 63
           +S T + LL +  +T  F G VA++DVSFS N  EI AI+G NGAGK+TL N I+G   P
Sbjct: 2   KSSTDSELLRLHGITKIFPGTVALSDVSFSVNKAEIHAIVGENGAGKSTLMNIISGSLLP 61

Query: 64  TVGRLTLRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIR 123
             G + L   +GK+  + R P  R +Q   ++   Q + L   ++V EN+ + +  +   
Sbjct: 62  DKGEIYL---EGKKVNI-RSP--RDAQNLGISIVHQELALCPHLTVAENIYIGRLPE--- 112

Query: 124 ASGFSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAM 183
                 A ++      +  +E + L     D V +      +  NL    Q+ +EIA+A+
Sbjct: 113 ----KSAKIVDFKKLNQMSQEVLSL----FDEVNIKPTD--KVANLNVAQQQIVEIAKAI 162

Query: 184 CTEPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLD 243
                +L LDEP + L+  ++  L  ++  ++ +  I +L I H +  +  ++D + VL 
Sbjct: 163 TFNCKLLILDEPTSALSEADAAVLFKIIKDLKAK-GISILYISHRLREIFELADRITVLR 221

Query: 244 YGRKISDGDPAFVKNDPAVIRAYLGEEEDEELPPE 278
            GR I+  + A   N   V+   +G E  E  PP+
Sbjct: 222 DGRYITTLNTA-ETNPDQVVSLMVGREIKEMYPPK 255



 Score = 52.0 bits (123), Expect = 3e-11
 Identities = 54/221 (24%), Positives = 102/221 (46%), Gaps = 18/221 (8%)

Query: 27  VNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTLRHADGKEFLLERMPGY 86
           V +VSF+ + GEI    G  G+G+T L   I G      G + L   +GK+  +      
Sbjct: 274 VQNVSFALHEGEILGFAGLVGSGRTELAQTICGILPKHCGEIYL---EGKKIEINSFEDA 330

Query: 87  RISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIAGLLGLPSYTRTEREAV 146
              +   V    +   LF  + V  N + A H K      +    LL         ++ +
Sbjct: 331 IRHKIGYVTEDRKQYGLFLKLPVAHN-VSAIHLK------YDYKRLL------IDRQKEL 377

Query: 147 DLAKYWLDRVRLLEFADWE-AGNLPYGAQRRLEIARAMCTEPVMLCLDEPAAGLNPRESG 205
            LA+ ++ ++ +   +  +   +L  G Q+++ IA+ +  +P +L LDEP  G++     
Sbjct: 378 SLAQEFVKKLNVKTSSYVQLVMSLSGGNQQKVMIAKWLAIKPRILILDEPTRGIDVGAKA 437

Query: 206 ELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGR 246
           E+  LL  +  ++ IG++LI  ++  ++ + D V+V+  GR
Sbjct: 438 EIHSLLRELA-KNGIGIILISSELPEIIGMCDRVLVMREGR 477


Lambda     K      H
   0.319    0.137    0.397 

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: 270
Number of extensions: 12
Number of successful extensions: 4
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: 294
Length of database: 499
Length adjustment: 30
Effective length of query: 264
Effective length of database: 469
Effective search space:   123816
Effective search space used:   123816
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 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