GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Desulfacinum infernum DSM 9756

Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate WP_337833398.1 BUB04_RS10875 amino acid ABC transporter ATP-binding protein

Query= SwissProt::P54537
         (240 letters)



>NCBI__GCF_900129305.1:WP_337833398.1
          Length = 257

 Score =  265 bits (677), Expect = 6e-76
 Identities = 138/247 (55%), Positives = 176/247 (71%), Gaps = 7/247 (2%)

Query: 1   MIKVEKLSKSFGKH-EVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTIT 59
           M++V  L K FG+   VL+ I   + +GEVV ++GPSGSGKST LRC+N LE+P  GTI 
Sbjct: 7   MVEVSNLHKVFGEDLHVLRGIDLEVKKGEVVVILGPSGSGKSTLLRCINFLEEPTAGTIR 66

Query: 60  IKDTEITKPK------TNTLKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQAA 113
           + D  I   K         L++R  +GM FQ F+LFPH T LENI+  PV V  +SK+ A
Sbjct: 67  VGDITIGAGKKTKEHNAKILEIRRRVGMCFQSFNLFPHMTALENIIEGPVTVLGQSKKEA 126

Query: 114 QEKAEDLLRKVGLFEKRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVK 173
              AE+LL  VGL +KR++YP+RLSGGQ+QRVAIAR+LAM PD+MLFDEPTSALDPE+VK
Sbjct: 127 IPYAEELLAWVGLTDKRDEYPSRLSGGQQQRVAIARSLAMKPDVMLFDEPTSALDPELVK 186

Query: 174 EVLQVMKELVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKRAQ 233
           EV+ VM+ L   GMT++ VTHEM FA++VADRVL MD G+ VE G P+E F +PK  R++
Sbjct: 187 EVVDVMERLAAEGMTIIAVTHEMHFARDVADRVLIMDGGVWVESGPPEEIFTNPKEARSR 246

Query: 234 DFLEKIL 240
            FL  IL
Sbjct: 247 QFLAHIL 253


Lambda     K      H
   0.317    0.134    0.368 

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: 188
Number of extensions: 8
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: 240
Length of database: 257
Length adjustment: 24
Effective length of query: 216
Effective length of database: 233
Effective search space:    50328
Effective search space used:    50328
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 (21.6 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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