GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Methanococcus aeolicus Nankai-3

Align Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate WP_011974043.1 MAEO_RS06850 ABC transporter ATP-binding protein

Query= TCDB::Q9HU32
         (257 letters)



>NCBI__GCF_000017185.1:WP_011974043.1
          Length = 238

 Score =  143 bits (361), Expect = 3e-39
 Identities = 89/236 (37%), Positives = 141/236 (59%), Gaps = 16/236 (6%)

Query: 3   EATPALEIRNLHKRYGDLE----VLKGISLTARDGDVISILGSSGSGKSTFLRCINLLEN 58
           E    +E +N+ K YG  E    VL+GI+L  ++G+ ++I+G SG GKST L  + LL+ 
Sbjct: 13  EKKELIEAKNIWKIYGGGEAKTVVLRGINLKIKEGEFVAIMGPSGCGKSTLLNILGLLDV 72

Query: 59  PHQGQILVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEA 118
           P++G + + G        K   + + + + + R R   GF+FQ FNL   ++ L+NV E 
Sbjct: 73  PNKGMVYIKG--------KKTTMFSENDRAVFR-RKISGFIFQQFNLINTLTALENV-EL 122

Query: 119 PRRVLGKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFD 178
           P  +  K+K   I+ A+ LL  + +  + + YP QLSGGQQQR AIAR L+  PK+I  D
Sbjct: 123 PLVLDEKNKNYRIKKAKKLLKIINLGHRENYYPNQLSGGQQQRVAIARALSNNPKIIFAD 182

Query: 179 EPTSALDPEMVQEVLNVIRALAE-EGRTMLLVTHEMSFARQVSSEVVFLHQGLVEE 233
           EPT  LD +  +EV+++++ L E EG T+++VTHE  FA+  +S ++ +  G + E
Sbjct: 183 EPTGNLDSKNSREVMDILKELNEKEGITVIMVTHEPEFAK-YASRIINMKDGEIVE 237


Lambda     K      H
   0.317    0.133    0.367 

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: 156
Number of extensions: 9
Number of successful extensions: 4
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: 257
Length of database: 238
Length adjustment: 24
Effective length of query: 233
Effective length of database: 214
Effective search space:    49862
Effective search space used:    49862
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: 46 (22.3 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