GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Streptococcus oralis 7747

Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate WP_000942251.1 HK29_RS01475 amino acid ABC transporter ATP-binding protein

Query= SwissProt::P54537
         (240 letters)



>NCBI__GCF_000382825.1:WP_000942251.1
          Length = 254

 Score =  252 bits (644), Expect = 4e-72
 Identities = 121/243 (49%), Positives = 183/243 (75%), Gaps = 3/243 (1%)

Query: 1   MIKVEKLSKSFGKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTITI 60
           M++VE ++K+FG+ +VL++++  + +G+VV ++GPSGSGK+TFLRCLN LEK + G +T+
Sbjct: 1   MLQVEHIAKTFGERQVLEDVNLQVNQGDVVVILGPSGSGKTTFLRCLNHLEKADSGRLTL 60

Query: 61  --KDTEITK-PKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQAAQEKA 117
             K  ++ K  K + L++R+    VFQH++LF +KT LENI+   +  +K  K+ A ++A
Sbjct: 61  AGKTYDLAKLSKKDILEIRQKTAFVFQHYNLFANKTALENILEGLIVARKVPKEEALKRA 120

Query: 118 EDLLRKVGLFEKRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEVLQ 177
           E  L KVGL   ++ YP++LSGGQ+QR+ IARA+A+ P+++L DEPTSALDPE+V +VL 
Sbjct: 121 ESALEKVGLLAYKDYYPSQLSGGQQQRIGIARAIAVKPEVILLDEPTSALDPELVGDVLD 180

Query: 178 VMKELVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKRAQDFLE 237
           V+K+L   G+TMV+VTHEMGFA++VA+ V+FMD G IVE+ NP +FF  P+ +R + FL 
Sbjct: 181 VLKQLAGEGVTMVVVTHEMGFARDVANHVIFMDGGRIVEENNPHDFFSRPQEERTKQFLA 240

Query: 238 KIL 240
           +IL
Sbjct: 241 RIL 243


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: 184
Number of extensions: 5
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: 254
Length adjustment: 24
Effective length of query: 216
Effective length of database: 230
Effective search space:    49680
Effective search space used:    49680
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 Sep 24 2021. 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