GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Slc7a1 in Dyella japonica UNC79MFTsu3.2

Align high affinity cationic amino acid transporter 1 (characterized)
to candidate N515DRAFT_2925 N515DRAFT_2925 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)

Query= CharProtDB::CH_091324
         (622 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2925
          Length = 480

 Score =  261 bits (667), Expect = 5e-74
 Identities = 153/439 (34%), Positives = 240/439 (54%), Gaps = 58/439 (13%)

Query: 20  DCSREESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALASVL 79
           DC    S L R L  + + ALG+G+ +G G++V+ G  A E+AGPA++ISF++AA+ S  
Sbjct: 17  DCHGGPS-LRRTLGKWGITALGIGAVIGTGIFVVTGQAAAEHAGPAVLISFMLAAICSGF 75

Query: 80  AGLCYGEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATFDEL 139
             LCY EF   +P +GS+Y Y+Y T+GEL A+  GWN++L Y I  S+VA +W+  F  L
Sbjct: 76  TALCYAEFATLIPISGSSYSYAYATLGELVAWFIGWNMVLEYGISASAVAASWTGYFTSL 135

Query: 140 IGKPIGEFSRQHMALNAPGVLAQTPDIF---------------AVIIIIILTGLLTLGVK 184
           +          H+ ++ P  L + P  F               AV I++ LT L  +G++
Sbjct: 136 L---------DHVGIHLPVALTEAPLAFKDGHLVTTGHLLNLPAVAIVLALTWLCYVGIR 186

Query: 185 ESAMVNKIFTCINVLVLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMP-- 242
           ES+ +N +   + V ++  +VV+G+      NW                      F+P  
Sbjct: 187 ESSGLNVLMVALKVGLIIVVVVAGYRYVDPANWH--------------------PFIPAE 226

Query: 243 -----FGFSGVLSGAATCFYAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGV 297
                +G+SG++ GAA  F+A++GF+  +T  +E KNPQK +P G + SL+IC + Y  +
Sbjct: 227 QEPGKYGWSGIMRGAAMVFFAYIGFEATSTAAQECKNPQKDLPFGTLVSLVICTVLYLAM 286

Query: 298 SAALTLMMPYFCLDIDSPLPGAFKHQ---GWEEAKYAVAIGSLCALSTSLLGSMFPMPRV 354
           +A LT ++PY  L    P+  A ++    GW   +  V IG++  LS+ +L  +   PR+
Sbjct: 287 AAVLTGLIPYTELGTSEPVVTAIRNHPELGW--LRLVVEIGAMIGLSSVILVMIIAQPRI 344

Query: 355 IYAMAEDGLLFKFLAKINNRTKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYS 414
              M+ DGLL     +I+ + +TP + TV +G   A++A +F L  L DL S+GTL+A+ 
Sbjct: 345 FMIMSRDGLLPPVFNRIHPKHRTPHLNTVITGIGIAILAAVFPLDLLADLTSMGTLIAFV 404

Query: 415 LVAACVLVLRY-QPEQPNL 432
            V A VL+LRY  PE P L
Sbjct: 405 AVCAGVLILRYTAPELPRL 423



 Score = 40.4 bits (93), Expect = 2e-07
 Identities = 39/131 (29%), Positives = 57/131 (43%), Gaps = 20/131 (15%)

Query: 474 LSPKNVEPSKFSGLIVNISAGLLAALIITVCIVAVLGREALAEGTLWAVFVMTGSVLLCM 533
           + PK+  P   + +I  I   +LAA +  + ++A L     + GTL A   +   VL   
Sbjct: 361 IHPKHRTPH-LNTVITGIGIAILAA-VFPLDLLADL----TSMGTLIAFVAVCAGVL--- 411

Query: 534 LVTGIIWRQPESKTKLSFKVP---FVPVLPVLSIFVNIYLMMQLDQGTWVRFAVWMLIGF 590
                I R    +    F+VP   FV    V S    +Y M   +   W+   +W  IG 
Sbjct: 412 -----ILRYTAPELPRLFRVPAAWFVCTAGVFSCLALLYFMAWFN---WLLMIIWTAIGL 463

Query: 591 TIYFGYGIWHS 601
            IYFGYG+ HS
Sbjct: 464 AIYFGYGMRHS 474


Lambda     K      H
   0.324    0.138    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: 743
Number of extensions: 31
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 622
Length of database: 480
Length adjustment: 36
Effective length of query: 586
Effective length of database: 444
Effective search space:   260184
Effective search space used:   260184
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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