GapMind for catabolism of small carbon sources

 

Alignments for a candidate for N515DRAFT_2924 in Flavobacterium ummariense DS-12

Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate WP_091525815.1 BM253_RS14680 amino acid permease

Query= uniprot:A0A1I1Y8J0
         (492 letters)



>NCBI__GCF_900115115.1:WP_091525815.1
          Length = 637

 Score =  324 bits (831), Expect = 5e-93
 Identities = 181/468 (38%), Positives = 269/468 (57%), Gaps = 51/468 (10%)

Query: 4   NLFATTQISPASADLPGGGAHGEATLKRALTARHLVLLGIGAIIGAGIFVITGQAAAEHA 63
           N+F    ++   A+L       E+ L + L+ + L+  GI AI+GAG+F   GQA+ +  
Sbjct: 2   NIFRKKNVTDILAELQANEGKKES-LGKFLSQKDLIFFGIAAIVGAGVFSTIGQASFD-G 59

Query: 64  GPAIVLSFVFAGIACALAALCYAEFAAMLPVSGSAYSYSYATLGEYVAWFVGWSLVLEYL 123
           GPA++  F+F  +AC  AA+ YAEFA+M+PVSGSAY+YSY   GE +AW +GWSL++EY 
Sbjct: 60  GPAVIFLFMFTALACGFAAMAYAEFASMVPVSGSAYTYSYVAFGEVIAWIIGWSLIMEYA 119

Query: 124 FTVATVAAGWSGYFNKLLALISGWIGHDVSLPQTLAAAPFTVVDGHIQATGMFIN----- 178
               T+A  WS YF  LL+        D+ LPQ +     +   G   A  +  N     
Sbjct: 120 VGNITLAISWSDYFTGLLS------NMDIHLPQWIQMDYLSANKGFNDAVALMANGKSFE 173

Query: 179 ---------------------------LPAVAIIAAITGLCYVGITQSAFVNSIIVAIKV 211
                                      +PA+AII  IT L Y G+ +S   ++I+V +K+
Sbjct: 174 NLPNNLQLAHIAWTTAPQIGSFHFVADIPALAIIVLITWLVYRGMKESRNASNIMVYVKL 233

Query: 212 TVILLFIAFATKYINPDNWHPFIPASEGASKYGWAGVGRAAAIVFFSYIGFDAVSTAAGE 271
            VI L +     Y++ DN+ PF P        G +GV +  + VFF+YIGFDA+ST A E
Sbjct: 234 AVIALVLIVGIFYVDTDNFDPFAP-------NGLSGVLKGVSAVFFAYIGFDAISTTAEE 286

Query: 272 AKNPQRDMPIGIIGSLILCTILYIIVAGILTGIADFRLLGTPEPVSTALDNYPSLHWLQI 331
            KNPQRD+P  +I S+I+CT+LYI +A +LTG+ +++ L   +P++   D   +L W   
Sbjct: 287 CKNPQRDLPRSMIWSIIICTLLYIAIALVLTGMVNYKQLNVGDPLAYVFDQV-NLKWFAG 345

Query: 332 IVVIGAVTGLSSVMLVMLMGQPRIFYSMARDGLIPAVFGRIHQKFRTPHVGTVVVGVLAA 391
           IV + AV  ++SV+LV  MGQPRI+ SM+RDGL+P  F ++H K+RTP   T+V G + A
Sbjct: 346 IVAVSAVVAMASVLLVFQMGQPRIWMSMSRDGLLPKKFSKVHPKYRTPSFATIVTGFVVA 405

Query: 392 ALGGLFNIGVLGEMVAMGTLLAFATVCIGVLVLRYTRPELPRA-FRVP 438
                 N+ ++ ++ ++GTL AF+ VC GVLVL+    ++PR  FR+P
Sbjct: 406 VPALFMNLTMVTDLCSIGTLFAFSLVCAGVLVLQ--DKDIPRGKFRIP 451



 Score = 34.3 bits (77), Expect = 1e-05
 Identities = 14/42 (33%), Positives = 23/42 (54%)

Query: 446 LGALACMALFLQSFLEHWRWMLAWIAIGQAIYFLYGYSHSKL 487
           LG + C+ +  +  + +W +   W+ IG  IYF Y   +SKL
Sbjct: 593 LGLICCIYMMAELTIWNWLYFSIWLIIGLLIYFSYSRFNSKL 634


Lambda     K      H
   0.328    0.141    0.441 

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: 851
Number of extensions: 46
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: 492
Length of database: 637
Length adjustment: 36
Effective length of query: 456
Effective length of database: 601
Effective search space:   274056
Effective search space used:   274056
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: 53 (25.0 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