GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proY in Methanospirillum lacunae Ki8-1

Align GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized)
to candidate WP_109967046.1 DK846_RS00935 amino acid permease

Query= SwissProt::P46349
         (469 letters)



>NCBI__GCF_003173355.1:WP_109967046.1
          Length = 518

 Score =  232 bits (592), Expect = 2e-65
 Identities = 144/474 (30%), Positives = 247/474 (52%), Gaps = 11/474 (2%)

Query: 7   GLKKELKTRHMTMISIAGVIGAGLFVGSGSVIHSTGPGAVVSYALAGLLVIFIMRMLGEM 66
           GL + ++    ++I+I G+IG+  ++GSG +I   GP  +  Y + GL++  +M+   E+
Sbjct: 37  GLNRGIRPWMASLIAIGGIIGSSYYLGSGYLISQMGPSVIFLYFIGGLVIYTVMQSFAEL 96

Query: 67  SAVNPTSGSFSQYAHDAIGPWAGFTIGWLYWFFWVIVIAIEAIAGAGIIQYWFHDIPLWL 126
               P  G+F  Y+ + I P      GW YWF W   I  EA+AG  I+  +F  +P+ +
Sbjct: 97  LVNVPRHGNFISYSAEFISPTWAVGTGWSYWFNWCAYIPSEAVAGGIIMHVFFDGVPVII 156

Query: 127 TSLILTIVLTLTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFAPGSEPVGFSN 186
            +++  I++T+ N+  V  FG  E   +LIK++  +AF IV    + G A     VGFS 
Sbjct: 157 WAIVFLILITILNLIHVGGFGFVESTLALIKIIHNVAFCIVAGLIVIGLAGTGTAVGFSV 216

Query: 187 L-----TGKGGFFPEGISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKATRSVVW 241
           L     T     FP G   +L  + +++ +F G+EIV +AA ET NP + V +A R+VV+
Sbjct: 217 LFPPGFTWTDAIFPAGFMILLANMALILVNFQGSEIVGLAASETQNPKKVVPRACRNVVY 276

Query: 242 RIIVFYVGSIAIVVALLPWNSANILESPFVAVLEHIGVPAAAQIMNFIVLTAVLSCLNSG 301
           RI+   +  I ++V +LP++ AN+ +S F   L   G    A I++FIVLTA  SC NSG
Sbjct: 277 RILRVDIIPILLLVMILPYSEANLQDSVFSMALAKYGFTEVAGILSFIVLTAAFSCANSG 336

Query: 302 LYTTSRMLYSLAERNEAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFS--PDTVFLF 359
            Y   R LY L+    AP+ F KL+K   P+ A +      +  + + +FS   + ++++
Sbjct: 337 FYGAVRALYGLSLEGMAPKTFAKLNKHCTPMYATLFTLVICWAVLGLWWFSNGENELYVW 396

Query: 360 LVNSSGAIALLVYLVIAVSQLKMRKKLEKT--NPEALKIKMWLFPFL-TYLTIIAICGIL 416
           L++ S     + ++ I  +Q+  R+++ +     E ++    L P++  ++ II     L
Sbjct: 397 LLSVSAFTGAICWISICWAQISFRRRVYQRGYTKEEIESPSPLSPWMPLFIGIILEIFAL 456

Query: 417 VSMAFIDSMRDELLLT-GVITGIVLISYLVFRKRKVSEKAAANPVTQQQPDILP 469
           V +AF + +R  L L+   I   ++I Y+  R  +        P  Q   ++ P
Sbjct: 457 VILAFNEDLRGSLYLSIPAILIPMIIYYIGMRTGRFKGIKVIEPDEQSFDELFP 510


Lambda     K      H
   0.326    0.140    0.417 

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: 639
Number of extensions: 28
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: 469
Length of database: 518
Length adjustment: 34
Effective length of query: 435
Effective length of database: 484
Effective search space:   210540
Effective search space used:   210540
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: 52 (24.6 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