GapMind for catabolism of small carbon sources

 

Alignments for a candidate for CCNA_00435 in Desulfoscipio geothermicus DSM 3669

Align Amino acid transporter (characterized, see rationale)
to candidate WP_092483642.1 BM299_RS10185 amino acid permease

Query= uniprot:A0A0H3C3Q5
         (483 letters)



>NCBI__GCF_900115975.1:WP_092483642.1
          Length = 484

 Score =  348 bits (894), Expect = e-100
 Identities = 190/478 (39%), Positives = 281/478 (58%), Gaps = 18/478 (3%)

Query: 8   VSFWTRRKAIDTITAGHADSHQLKKTLSWPHLVALGVGAIVGTGIYTLTGVGAG-LAGPG 66
           +S W ++     +     +   L  TL    L ALGVGA++GTGI+ LTGV A   AGPG
Sbjct: 1   MSVWRKKPVEQVLADKKKNKRGLVPTLGVADLTALGVGAVIGTGIFVLTGVAAANYAGPG 60

Query: 67  VILSFLIAGAVCACAALCYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVC 126
           V+ SF+++G     AA+ YAEL   IP++GSAYT+SY ++GE +AW VGW+LILEY +  
Sbjct: 61  VVFSFILSGIAATLAAMVYAELGAAIPSAGSAYTFSYVSLGEIIAWLVGWNLILEYLVAA 120

Query: 127 AAVAVGWSAHAHGLFKMIGF--PDALLAGPHQGGLINMPAVFISMAVAGLLALGTRESAT 184
            AV++GWS++   L + +G   P A  + P  GG++N+PA  I + + GL+  GT+ S T
Sbjct: 121 GAVSIGWSSYMGDLLQSVGITLPAAFTSSPFDGGIVNLPAALIVLVITGLIITGTQHSTT 180

Query: 185 VNMVLVFVKIIALIVFVVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADAAKVGVMAAASL 244
            N ++V  K+ A+ +F+ L +   N A++ P +P G                GV   A++
Sbjct: 181 ANKIIVVAKLAAIALFIALGVQHINPANWRPVLPYGIS--------------GVFHGAAI 226

Query: 245 IFFAFYGFDAVSTAAEETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGASRTEVFSKSE 304
           +FFA+ GFDAV+TA+EE KNP+RDL  GI+ ++ + T +Y++VA +  G  +    + + 
Sbjct: 227 VFFAYIGFDAVATASEEVKNPQRDLPRGIIWTLVISTLLYIVVAGILTGMVKYTNLNTA- 285

Query: 305 APLVFILESLNHGKIAQLVALAAVIALPTVILAFMYGQSRIFFVMARDGLLPRALSKVNA 364
           +P+   L        + LV++ A+  L +V+L  MYGQSRIFF MARD LLP     ++ 
Sbjct: 286 SPVATALLRAGIPWASALVSVGALAGLTSVLLVAMYGQSRIFFAMARDDLLPPIFDWLHP 345

Query: 365 KTGTPVMMTLLTGVLAAVISGLLSLKDIAELANAGTLWAFIAVGASVILLRLREPNRPRV 424
           +  TPV  +++ GVL A+I   L +  +AELAN GTL AFIAV    I+LR   P+  R 
Sbjct: 346 RLRTPVWDSIIIGVLVALIGAFLPIGLVAELANIGTLTAFIAVSTGAIILRRTNPDLRRP 405

Query: 425 FSTPLWPIVAPAGILGCLYLFLSLPGKTQLYFLYAHLIGAVVYLAYGMRKSVLAQQER 482
           F  P  P +    I+   YL ++LP  T + F+    IG VVY  YG RKS LA++ +
Sbjct: 406 FRLPWMPAIPVLTIISAGYLAINLPPLTWVRFIAWVAIGLVVYWLYGYRKSKLARESQ 463


Lambda     K      H
   0.326    0.138    0.415 

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: 667
Number of extensions: 38
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: 483
Length of database: 484
Length adjustment: 34
Effective length of query: 449
Effective length of database: 450
Effective search space:   202050
Effective search space used:   202050
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 Apr 09 2024. 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