GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ansP in Bacillus altitudinis 41KF2b

Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate WP_008347408.1 BA79_RS16380 amino acid permease

Query= TCDB::P40812
         (497 letters)



>NCBI__GCF_000691145.1:WP_008347408.1
          Length = 448

 Score =  330 bits (846), Expect = 6e-95
 Identities = 170/438 (38%), Positives = 258/438 (58%), Gaps = 13/438 (2%)

Query: 30  MGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRALGELVLHRP 89
           + NR VQ+IAIGG IGTGLFLG+G  +Q+AGP++   YLI G+  FF++RALGEL+L + 
Sbjct: 10  LSNRHVQLIAIGGTIGTGLFLGSGKAIQLAGPSIIFAYLIVGMAIFFVMRALGELLLSKA 69

Query: 90  SSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDVPQWVFAL 149
              S    A ++LG  A++V GW Y+  W MT + D+ AV +Y+ YW    D+PQW+ A+
Sbjct: 70  GYQSLTDIAEDYLGPWASFVTGWTYWFCWIMTAMADVIAVGVYVQYWF---DIPQWIPAI 126

Query: 150 GALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFLGTGQPLEGNATGFHLIT 209
             L I+   N++ VK F EMEFWFALIKV+ I++ + VG + L  G   +        + 
Sbjct: 127 ICLLILLGFNLLTVKLFGEMEFWFALIKVITILLLIGVGIVLLIIGFQTDAGPVTVTNLW 186

Query: 210 DNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVIWRIGLFYV 269
            +GG FP+G+   L+  Q V+FA+  +ELVG +A E  +PQK +P AIN +  RI  FYV
Sbjct: 187 SHGGLFPNGVTGFLLSFQMVIFAYVGVELVGVSAAETANPQKNIPSAINKIPLRILFFYV 246

Query: 270 GSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNSGLYCTGRI 329
           G++ +L+ + PW    A +SPFV  F  +G+P    ++N VVLT+A S+ NSG++ T RI
Sbjct: 247 GAIFVLLCINPWTELSASESPFVKTFGLIGIPVAAGLINFVVLTSAASACNSGMFSTSRI 306

Query: 330 LRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFEIVLNFASLGI 389
           L ++S     P    ++++  VP   +  + +V  VG  L+ L+P + F IV   +++  
Sbjct: 307 LYNLSHQKQGPASFGRLNKHAVPSNALFVSTIVVSVGALLSKLIPEQAFGIVTTISAICF 366

Query: 390 IASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLVLMAFDYPNGTY 449
           I  W+ I++C ++ ++   E   A  +FK P  PF +   L+   ++LV+M F       
Sbjct: 367 IWVWSIILICHLKYKKTRPELHKAS-TFKAPFTPFVNIAVLVLFAAILVIMLF------- 418

Query: 450 TIASLPLIAILLVAGWFG 467
             A     A+LL   WFG
Sbjct: 419 --ADATRPALLLTPVWFG 434


Lambda     K      H
   0.328    0.140    0.434 

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: 602
Number of extensions: 35
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: 497
Length of database: 448
Length adjustment: 33
Effective length of query: 464
Effective length of database: 415
Effective search space:   192560
Effective search space used:   192560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. 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