GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Desulfacinum infernum DSM 9756

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc04256
         (361 letters)



>NCBI__GCF_900129305.1:WP_073037934.1
          Length = 365

 Score =  273 bits (699), Expect = 4e-78
 Identities = 156/361 (43%), Positives = 220/361 (60%), Gaps = 21/361 (5%)

Query: 4   VSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIK 63
           + +RD+  ++G V  +  ++  ++ G+ LV+LG SGCGK+TLL  IAGL  V+ G I I 
Sbjct: 3   IEIRDVRKDYGRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIHIA 62

Query: 64  DRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQI 123
             +VT   P  R I MVFQSYAL+P + V +N+ FGLKV K+P  EIE+R+KR  ++L +
Sbjct: 63  GTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLLGL 122

Query: 124 QPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSL 183
              L  KP ELSGG +QRVA+GRA++ +  V L DEPLSNLDAKLR+ +R EI  L + L
Sbjct: 123 SGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQRRL 182

Query: 184 KNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFR 243
             TMIYVTHDQ+EA+T+ADRI +M+ G I Q   P   Y  P N FVA FIG+P MN   
Sbjct: 183 GITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNIV- 241

Query: 244 GEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPG---QKVVLGLRPEHVKVDEARDGEPTH 300
             + P  G + +  GG             L PG    + + G+RPE++++  A  G+P  
Sbjct: 242 -PLCPTQGGAALEPGG-----------RLLFPGMDPDRYLFGIRPENLRL--AESGQP-- 285

Query: 301 QAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAESENR 360
            A+V   E +G+D  +     GQ + VR  G+R    G+ V L++D G  ++FDA ++ R
Sbjct: 286 -AMVTGREYLGSDTFVSCEIHGQEVIVRTRGRRNIREGTVVHLTWDPGDVNLFDARTQER 344

Query: 361 L 361
           +
Sbjct: 345 V 345


Lambda     K      H
   0.320    0.137    0.392 

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: 380
Number of extensions: 15
Number of successful extensions: 2
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: 361
Length of database: 365
Length adjustment: 29
Effective length of query: 332
Effective length of database: 336
Effective search space:   111552
Effective search space used:   111552
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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