GapMind for catabolism of small carbon sources

 

Alignments for a candidate for N515DRAFT_2924 in Desulfoscipio geothermicus DSM 3669

Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate WP_092483642.1 BM299_RS10185 amino acid permease

Query= uniprot:A0A1I1Y8J0
         (492 letters)



>NCBI__GCF_900115975.1:WP_092483642.1
          Length = 484

 Score =  398 bits (1023), Expect = e-115
 Identities = 209/452 (46%), Positives = 285/452 (63%), Gaps = 23/452 (5%)

Query: 38  LVLLGIGAIIGAGIFVITGQAAAEHAGPAIVLSFVFAGIACALAALCYAEFAAMLPVSGS 97
           L  LG+GA+IG GIFV+TG AAA +AGP +V SF+ +GIA  LAA+ YAE  A +P +GS
Sbjct: 32  LTALGVGAVIGTGIFVLTGVAAANYAGPGVVFSFILSGIAATLAAMVYAELGAAIPSAGS 91

Query: 98  AYSYSYATLGEYVAWFVGWSLVLEYLFTVATVAAGWSGYFNKLLALISGWIGHDVSLPQT 157
           AY++SY +LGE +AW VGW+L+LEYL     V+ GWS Y   LL  +       ++LP  
Sbjct: 92  AYTFSYVSLGEIIAWLVGWNLILEYLVAAGAVSIGWSSYMGDLLQSVG------ITLPAA 145

Query: 158 LAAAPFTVVDGHIQATGMFINLPAVAIIAAITGLCYVGITQSAFVNSIIVAIKVTVILLF 217
             ++PF   DG I      +NLPA  I+  ITGL   G   S   N IIV  K+  I LF
Sbjct: 146 FTSSPF---DGGI------VNLPAALIVLVITGLIITGTQHSTTANKIIVVAKLAAIALF 196

Query: 218 IAFATKYINPDNWHPFIPASEGASKYGWAGVGRAAAIVFFSYIGFDAVSTAAGEAKNPQR 277
           IA   ++INP NW P +P       YG +GV   AAIVFF+YIGFDAV+TA+ E KNPQR
Sbjct: 197 IALGVQHINPANWRPVLP-------YGISGVFHGAAIVFFAYIGFDAVATASEEVKNPQR 249

Query: 278 DMPIGIIGSLILCTILYIIVAGILTGIADFRLLGTPEPVSTALDNYPSLHWLQIIVVIGA 337
           D+P GII +L++ T+LYI+VAGILTG+  +  L T  PV+TAL     + W   +V +GA
Sbjct: 250 DLPRGIIWTLVISTLLYIVVAGILTGMVKYTNLNTASPVATALLR-AGIPWASALVSVGA 308

Query: 338 VTGLSSVMLVMLMGQPRIFYSMARDGLIPAVFGRIHQKFRTPHVGTVVVGVLAAALGGLF 397
           + GL+SV+LV + GQ RIF++MARD L+P +F  +H + RTP   ++++GVL A +G   
Sbjct: 309 LAGLTSVLLVAMYGQSRIFFAMARDDLLPPIFDWLHPRLRTPVWDSIIIGVLVALIGAFL 368

Query: 398 NIGVLGEMVAMGTLLAFATVCIGVLVLRYTRPELPRAFRVPVPWIVCPLGALACMALFLQ 457
            IG++ E+  +GTL AF  V  G ++LR T P+L R FR+P    +  L  ++   L + 
Sbjct: 369 PIGLVAELANIGTLTAFIAVSTGAIILRRTNPDLRRPFRLPWMPAIPVLTIISAGYLAIN 428

Query: 458 SFLEHWRWMLAWIAIGQAIYFLYGYSHSKLRK 489
                W   +AW+AIG  +Y+LYGY  SKL +
Sbjct: 429 LPPLTWVRFIAWVAIGLVVYWLYGYRKSKLAR 460


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: 764
Number of extensions: 35
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: 492
Length of database: 484
Length adjustment: 34
Effective length of query: 458
Effective length of database: 450
Effective search space:   206100
Effective search space used:   206100
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