GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Bacillus altitudinis 41KF2b

Align Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized)
to candidate WP_008347408.1 BA79_RS16380 amino acid permease

Query= TCDB::P24207
         (458 letters)



>NCBI__GCF_000691145.1:WP_008347408.1
          Length = 448

 Score =  372 bits (956), Expect = e-107
 Identities = 178/442 (40%), Positives = 279/442 (63%), Gaps = 3/442 (0%)

Query: 19  LHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYGVAGIIAFLIMRQLGEMV 78
           L R L NRH+QLIA+GG IGTGLFLG G AIQ+AGP+++  Y + G+  F +MR LGE++
Sbjct: 6   LKRDLSNRHVQLIAIGGTIGTGLFLGSGKAIQLAGPSIIFAYLIVGMAIFFVMRALGELL 65

Query: 79  VEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWFPDVPTWIW 138
           + +    S    A  Y GP+A F++GW YW  +++  MA++ A G+Y+QYWF D+P WI 
Sbjct: 66  LSKAGYQSLTDIAEDYLGPWASFVTGWTYWFCWIMTAMADVIAVGVYVQYWF-DIPQWIP 124

Query: 139 AAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMIGFGLWLLFSGHGGEKA--SIDN 196
           A    +I+   NL+ V+L+GE EFWFALIKV+ I+ +IG G+ LL  G   +    ++ N
Sbjct: 125 AIICLLILLGFNLLTVKLFGEMEFWFALIKVITILLLIGVGIVLLIIGFQTDAGPVTVTN 184

Query: 197 LWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKAVNQVVYRILLF 256
           LW +GG F  G  G +LS  +++F++ G+EL+G++AAE  +P+K+IP A+N++  RIL F
Sbjct: 185 LWSHGGLFPNGVTGFLLSFQMVIFAYVGVELVGVSAAETANPQKNIPSAINKIPLRILFF 244

Query: 257 YIGSLVVLLALYPWVEVKSNSSPFVMIFHNLDSNVVASALNFVILVASLSVYNSGVYSNS 316
           Y+G++ VLL + PW E+ ++ SPFV  F  +   V A  +NFV+L ++ S  NSG++S S
Sbjct: 245 YVGAIFVLLCINPWTELSASESPFVKTFGLIGIPVAAGLINFVVLTSAASACNSGMFSTS 304

Query: 317 RMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAITSLVVLINYLLPQKAFGLLMALVVA 376
           R+L+ LS Q   P    R+++  VP N+L +S  + S+  L++ L+P++AFG++  +   
Sbjct: 305 RILYNLSHQKQGPASFGRLNKHAVPSNALFVSTIVVSVGALLSKLIPEQAFGIVTTISAI 364

Query: 377 TLLLNWIMICLAHLRFRAAMRRQGRETQFKALLYPFGNYLCIAFLGMILLLMCTMDDMRL 436
             +  W +I + HL+++       + + FKA   PF N   +     IL++M   D  R 
Sbjct: 365 CFIWVWSIILICHLKYKKTRPELHKASTFKAPFTPFVNIAVLVLFAAILVIMLFADATRP 424

Query: 437 SAILLPVWIVFLFMAFKTLRRK 458
           + +L PVW  FLF+ +   +R+
Sbjct: 425 ALLLTPVWFGFLFLIYARKKRR 446


Lambda     K      H
   0.329    0.143    0.447 

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: 581
Number of extensions: 24
Number of successful extensions: 3
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: 458
Length of database: 448
Length adjustment: 33
Effective length of query: 425
Effective length of database: 415
Effective search space:   176375
Effective search space used:   176375
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 (21.8 bits)
S2: 51 (24.3 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