GapMind for catabolism of small carbon sources

 

Alignments for a candidate for yveA in Lactobacillus silagei IWT126

Align Aspartate-proton symporter; L-aspartate transporter (characterized)
to candidate WP_089137194.1 CES79_RS10845 APC family permease

Query= SwissProt::O07002
         (520 letters)



>NCBI__GCF_002217945.1:WP_089137194.1
          Length = 540

 Score =  310 bits (794), Expect = 9e-89
 Identities = 176/513 (34%), Positives = 283/513 (55%), Gaps = 26/513 (5%)

Query: 9   KSMSLFDLILIGMGAIFGSAWLFAVSNVASKAGPSGAFSWILGGAIILLIGLVYAELGAA 68
           K ++LF L+++ +G++ GS WLF        AGP+  FSWI+GG +I  I   Y E+GA 
Sbjct: 7   KKINLFQLVMLALGSLIGSGWLFGSWEATKIAGPAAIFSWIIGGLVIGSIAYDYVEIGAM 66

Query: 69  LPRTGGIIRYPVYSHGHLVGYLISFVTIVAYTSLISIEVTAVRQYV-------AYWFPGL 121
            P +GG+ +Y  YSHG L+G++ ++   V+  +LI IE  A  QY+       A+W    
Sbjct: 67  FPESGGMSKYAQYSHGSLLGFIAAWANWVSLITLIPIEAVAAVQYMSTWPWSWAHWTHHF 126

Query: 122 TIKGSDSPTISGWILQFALLCLFFLLNYWSVKTFAKANFIISIFKYIVPI-TIIIVLIFH 180
              G    T SG ++ F  + +F  LN+WSV    +   +IS+FK  +P+ TI+++ +  
Sbjct: 127 LSNGVI--TNSGLLIVFGFILVFTALNFWSVTILTRFTSLISVFKIGIPLLTIVMLTMSG 184

Query: 181 FQPENL--SVQGFAPFGFTGIQAAISTGGVMFAYLGLHPIVSVAGEVQNPKRNIPIALII 238
           F P N   ++  F P+G   I  A S  G++F++     ++++ GE+++PK+NI   + I
Sbjct: 185 FHPGNYGSNLHDFMPYGSAPIFTATSAAGIIFSFDAFQTVINMGGEIEHPKKNIGRGITI 244

Query: 239 CIIVSTIIYTVLQVTFIGAIPTETLKH-GWPAIGREFSLPFKDIAVMLGLGWLATLVILD 297
            +++S I+Y +LQ TFI AIP + +   GW  I   F+ PF D+A++LG+ WL+ L+ +D
Sbjct: 245 SLLISGILYVILQSTFITAIPPKMIAATGWHGI--VFNSPFADMAILLGIHWLSVLLYMD 302

Query: 298 AILSPGGNGNIFMNTTSRLVYAWARNGTLFGIFSKVNKDTGTPRASLWLSFALSIFWTLP 357
           A +SP G G  F+  T+R ++A   N  +     K+N   G PR ++ ++  LS+     
Sbjct: 303 AFVSPFGTGVSFVANTARALFAMEGNRHVPHFLGKINLKYGIPRNAMVVNTVLSMVMVSV 362

Query: 358 FPSWNALVNVCSVALILSYAIAPISSAALRVNAKDLNRPFYLKGMSIIGPLSFIFTAFIV 417
           F SW  L  V S A +++Y   P+++ +LR     L RP  LK +  I P+SF+  +   
Sbjct: 363 FRSWAVLATVLSTATLIAYLTGPVTAVSLRKMGSKLYRPIRLKHLPWIAPVSFVLASLAT 422

Query: 418 YWSGWKTVSWLLGSQLVMFLIYLCFSKYTPKE----DVSLAQQLKSAWWLIGFYIMMLIF 473
           YW+ W T      +  V+F+I L    Y   E     VS  Q  K++ W+IG+ I + I 
Sbjct: 423 YWAMWPT------TVEVIFIILLGLPFYFYYEWRNHFVSTKQAFKASGWMIGYLIFISIM 476

Query: 474 SYIGSFG-HGLGIISNPVDLILVAIGSLAIYYW 505
           SYIGS   +G   I  P+D +++ I SL  Y+W
Sbjct: 477 SYIGSHQFNGQNWIPYPLDFVVIIIASLGFYWW 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: 943
Number of extensions: 47
Number of successful extensions: 5
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: 540
Length adjustment: 35
Effective length of query: 485
Effective length of database: 505
Effective search space:   244925
Effective search space used:   244925
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