GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Desulfacinum infernum DSM 9756

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

Query= reanno::Smeli:SM_b21216
         (360 letters)



>NCBI__GCF_900129305.1:WP_073037934.1
          Length = 365

 Score =  267 bits (683), Expect = 3e-76
 Identities = 151/347 (43%), Positives = 212/347 (61%), Gaps = 11/347 (3%)

Query: 4   LEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIG 63
           +EIR++RK YG V+ ++G+  ++E G+ LV+LG SGCGK+TLL +IAGL   + G I I 
Sbjct: 3   IEIRDVRKDYGRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIHIA 62

Query: 64  ERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLLQI 123
              V  + P  R+I+MVFQSYAL+P+L+V  NI FGL++R+VP  E ++ ++    LL +
Sbjct: 63  GTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLLGL 122

Query: 124 ENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQML 183
              LD KP +LSGG +QRVA+GRA++    V L DEPLSNLDAKLR  MR E+  L + L
Sbjct: 123 SGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQRRL 182

Query: 184 RTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMNILD 243
             T++YVTHDQ+EAMT+A RI +MRDG+I Q  +P+  Y+RPA  +VA F+G+PPMNI+ 
Sbjct: 183 GITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNIVP 242

Query: 244 AEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLTASVEVV 303
              T  G  +E    +L     F G      R   GIRPE LRLA   +   +T      
Sbjct: 243 LCPTQGGAALEPGGRLL-----FPG--MDPDRYLFGIRPENLRLAESGQPAMVTGR---- 291

Query: 304 ELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFD 350
           E  G +   +  +  Q +      R  +  G+    T+D   ++LFD
Sbjct: 292 EYLGSDTFVSCEIHGQEVIVRTRGRRNIREGTVVHLTWDPGDVNLFD 338


Lambda     K      H
   0.320    0.136    0.385 

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: 365
Number of extensions: 17
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: 360
Length of database: 365
Length adjustment: 29
Effective length of query: 331
Effective length of database: 336
Effective search space:   111216
Effective search space used:   111216
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