GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Psest_0084 in Marinobacter algicola DG893

Align TRAP transporter (characterized, see rationale)
to candidate WP_007151845.1 MDG893_RS01040 TRAP transporter permease

Query= uniprot:A8LI82
         (743 letters)



>NCBI__GCF_000170835.1:WP_007151845.1
          Length = 865

 Score =  222 bits (565), Expect = 7e-62
 Identities = 120/309 (38%), Positives = 179/309 (57%), Gaps = 12/309 (3%)

Query: 185 DLVLAICGVAVATYLITIYGTLMRNSTGTPFAPIGIS-IAAVAGTALIMELTRRVAGMAL 243
           D +LA+     A+YL   Y  L       P +PI    I A+ G  L++E TRR  G+ L
Sbjct: 101 DWILALAAAFAASYLYLFYDQLATR----PGSPITQDLIIALGGLVLLLEATRRALGLPL 156

Query: 244 IVIAGIFLAYVFVGQYLPGFLNAPAVTWQRFFSQVYTDA-GILGPTTAVSSTYIILFIIF 302
            V+AG+FL Y   G Y+P  ++    +  +  S ++    G+ G    VS++++ LF++F
Sbjct: 157 TVVAGVFLIYALAGPYMPDVISHKGASLSKLSSHMWLGTEGVFGVALGVSTSFVFLFVLF 216

Query: 303 AAFLQASKVGDYFVNFAFAAAGQSRGGPAKVAIFASGLMGMINGTSAGNVVATGSLTIPL 362
            A L+ +  G+YF+  A+A  G  RGGPAK A+ +SGL G+I+G+S  NVV TG+ TIPL
Sbjct: 217 GALLERAGAGNYFIQVAYAMLGHMRGGPAKAAVVSSGLSGVISGSSIANVVTTGTFTIPL 276

Query: 363 MKKVGYHKKTAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIALAAIIPAILYFV 422
           MK+VG+    AGAVE AAST GQ+ PPIMGA AF+M E  GI Y E+   AI+PA++ +V
Sbjct: 277 MKRVGFPATKAGAVEVAASTNGQLTPPIMGAAAFLMVEYVGISYLEVIKHAILPALISYV 336

Query: 423 SVYFMVDLEAAKLGMRGMSRDELPKF-NKMVRQVYLFLPIIILIYALFMGYSVIRAGTLA 481
           ++ ++V LEA KL M+G+ R   P    +M+  V + + +  + + ++ G      G L 
Sbjct: 337 ALIYIVHLEACKLKMKGIERPNRPTLAQRMLNWVVILIGLSAITFIVYYG-----IGWLK 391

Query: 482 TVAAAVVSW 490
            V      W
Sbjct: 392 VVLGEAAVW 400



 Score =  156 bits (394), Expect = 5e-42
 Identities = 96/277 (34%), Positives = 146/277 (52%), Gaps = 25/277 (9%)

Query: 441 SRDELPKFNKMVRQ-VYLFLPIIILIYAL----------------FMGYSVIRAGTLATV 483
           S D LP+    V+  +Y  LP+++L++ L                FM + VI    L   
Sbjct: 431 SMDTLPEVGPTVKTGLYFLLPVVVLVWCLTVERFSPQLSAFWATVFMIFIVITQQPLKAF 490

Query: 484 AAAVVSWFTPFRMGPRSIAKAFEIAGTMSVQIIAVCACAGIIVGVISLTGVGARFSAVLL 543
                ++ T  + G   +  +    G   V I    A AGI+VG ++LTG+G   +  + 
Sbjct: 491 FREKGNFLTETKTGFVDLTHSLVTGGRNMVGIGVATATAGIVVGTVTLTGIGLVMTQFVE 550

Query: 544 GIADTSQLLALFFAMCIAILLGMGMPTTAAYAVAASVVAPGLVQLG------IPLLTAHF 597
            I+  + LL L F   I+++LGMG+PTTA Y V ++++AP +V LG      +PL+  H 
Sbjct: 551 FISGGNLLLMLVFTALISLILGMGLPTTANYIVVSTLMAPVIVTLGAQNGLLVPLIAVHL 610

Query: 598 FVFYFAVLSAITPPVALASYAAAGISGANPMETSVTSFKIGIAAFIVPFMFFYNSAILMD 657
           FVFYF +L+  TPPV LA+YAAA ISGA+P+ T V  F   I   I+PFMF +N+ +L+ 
Sbjct: 611 FVFYFGILADDTPPVGLAAYAAAAISGADPIRTGVQGFTYDIRTAILPFMFIFNTQLLLI 670

Query: 658 GT--WFEVLRAGATAVVGVFFLSSGVQGWFMGGRAAW 692
           G   W ++L   A+AV  +   S+  QG++      W
Sbjct: 671 GLTGWVDLLVTIASAVTAMLVFSAATQGYWFTKSYKW 707


Lambda     K      H
   0.327    0.140    0.419 

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: 1633
Number of extensions: 95
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 743
Length of database: 865
Length adjustment: 41
Effective length of query: 702
Effective length of database: 824
Effective search space:   578448
Effective search space used:   578448
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: 55 (25.8 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