GapMind for catabolism of small carbon sources

 

Aligments for a candidate for yveA in Paraburkholderia bryophila 376MFSha3.1

Align Aspartate-proton symporter; L-aspartate transporter (characterized)
to candidate H281DRAFT_05687 H281DRAFT_05687 amino acid/polyamine/organocation transporter, APC superfamily

Query= SwissProt::O07002
         (520 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_05687 H281DRAFT_05687 amino
           acid/polyamine/organocation transporter, APC superfamily
          Length = 531

 Score =  381 bits (978), Expect = e-110
 Identities = 199/515 (38%), Positives = 307/515 (59%), Gaps = 15/515 (2%)

Query: 4   QGNFQKSMSLFDLILIGMGAIFGSAWLFAVSNVASKAGPSGAFSWILGGAIILLIGLVYA 63
           + + Q+++  F L+L G+G+I GS WLF     A  AGP+   +WI+G  +IL I L YA
Sbjct: 2   KSSIQRNIGPFALMLTGLGSIIGSGWLFGAWKAAKIAGPASICAWIIGAVVILAIALTYA 61

Query: 64  ELGAALPRTGGIIRYPVYSHGHLVGYLISFVTIVAYTSLISIEVTAVRQYVAYW----FP 119
           ELGA  P +GG++RY  YSHG LVG++ ++   +A  S+I IE  A  QY++ W      
Sbjct: 62  ELGAMFPESGGMVRYARYSHGALVGFISAWANWIAIVSVIPIEAEASIQYMSTWPYEWAH 121

Query: 120 GLTIKGSDSPTISGWILQFALLCLFFLLNYWSVKTFAKANFIISIFKYIVP-ITIIIVLI 178
            L + GS   T +G +L  AL+ ++FLLNYW VK FA+AN  I+IFK+++P  TI+ +++
Sbjct: 122 ALFVDGS--LTTNGLLLSAALVIIYFLLNYWGVKLFARANSAITIFKFLIPGATILGLML 179

Query: 179 FHFQPENLS-VQGFAPFGFTGIQAAISTGGVMFAYLGLHPIVSVAGEVQNPKRNIPIALI 237
             F  EN      FAP+G++ +  A++T G++FA+ G    +++AGE +NP +++P A+I
Sbjct: 180 TGFHKENFGETSTFAPYGWSAVLTAVATSGIVFAFNGFQSPINLAGEARNPAKSVPFAVI 239

Query: 238 ICIIVSTIIYTVLQVTFIGAIPTETLKHGWPAIGREFSLPFKDIAVMLGLGWLATLVILD 297
             I+++ +IY +LQV +IGA+    +  GW      F+ PF ++A+ L L WLA L+ +D
Sbjct: 240 GSILLALVIYVLLQVAYIGAVSPADVMKGWSHFN--FASPFAELAIALNLNWLAILLYVD 297

Query: 298 AILSPGGNGNIFMNTTSRLVYAWARNGTLFGIFSKVNKDTGTPRASLWLSFALSIFWTLP 357
           A +SP G G  +M TT+R++YA  RN T+  IF  V+   G PR ++W +  +S  +   
Sbjct: 298 AFVSPSGTGTTYMATTTRMIYAMERNNTMPKIFGNVHPFYGVPRPAMWFNLLVSFIFLFF 357

Query: 358 FPSWNALVNVCSVALILSYAIAPISSAALRVNAKDLNRPFYLKGMSIIGPLSFIFTAFIV 417
           F  W++L  V SVA ++SY   PIS  ALR  A DL RP ++ GM +I P +F+  + I+
Sbjct: 358 FRGWSSLAAVISVATVISYLTGPISLMALRRAATDLERPLHIPGMQVIAPFAFVCASLIL 417

Query: 418 YWSGWKTVSWLLGSQLVMFLIYLCFSKYTPKEDVSLAQQLKSAWWLIGFYIMMLIFSYIG 477
           YW+ W     ++   +V   +Y  F            + LK+AWWL+ +  +M I S IG
Sbjct: 418 YWAKWPLTGEIILLMVVALPVYFYFQ--AKSGFAGWGRDLKAAWWLVAYLPIMAILSLIG 475

Query: 478 S--FGHGLGIISNPVDLILVAIGSLAIYYWAKYTG 510
           S  FG G GI+    D+++V   SL  YYW  ++G
Sbjct: 476 SKEFG-GHGILPYGWDMLVVIAFSLVFYYWGVHSG 509


Lambda     K      H
   0.328    0.143    0.451 

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: 978
Number of extensions: 47
Number of successful extensions: 6
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: 520
Length of database: 531
Length adjustment: 35
Effective length of query: 485
Effective length of database: 496
Effective search space:   240560
Effective search space used:   240560
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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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