GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Rhizorhabdus wittichii RW1

Align ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4773
         (244 letters)



>NCBI__GCF_000016765.1:WP_012048833.1
          Length = 241

 Score =  262 bits (670), Expect = 4e-75
 Identities = 134/242 (55%), Positives = 173/242 (71%), Gaps = 2/242 (0%)

Query: 1   MISIKSINKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDIVV 60
           MI +  + KWYG +  L + S +V +GE IV+CGPSGSGKSTLI+C+N LE   +G I +
Sbjct: 1   MIHMAGVGKWYGGYHALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRI 60

Query: 61  DGTSIADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATKKGLQL 120
               +   +  L ++R+RVGMVFQ F LFPHLTI EN  +A +KV G +++ A     +L
Sbjct: 61  GEDEVRPDRRVLQRIRARVGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALAREL 120

Query: 121 LERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVMV 180
           LERV ++  A K+P QLSGGQQQR AIARALAM P ++LFDEPTSALD EMV EVLD+M 
Sbjct: 121 LERVRIADQADKYPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKEVLDIMK 180

Query: 181 QLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDINARAERTQHFLNK 240
            LA EG+TM+CVTHEMGFAR+VADR+IFMD G+I+E     +FF       ERT+ FL++
Sbjct: 181 ALATEGITMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFF--TAPCHERTRAFLSR 238

Query: 241 IL 242
           +L
Sbjct: 239 LL 240


Lambda     K      H
   0.321    0.136    0.394 

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: 178
Number of extensions: 6
Number of successful extensions: 1
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: 244
Length of database: 241
Length adjustment: 23
Effective length of query: 221
Effective length of database: 218
Effective search space:    48178
Effective search space used:    48178
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 (21.9 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