GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_05687
          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:

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