GapMind for catabolism of small carbon sources

 

Alignments for a candidate for actP in Paenisporosarcina indica PN2

Align Monocarboxylic acid transporter (characterized)
to candidate WP_075619342.1 GY23_RS11345 sodium/solute symporter

Query= SwissProt::Q8NS49
         (551 letters)



>NCBI__GCF_001939075.1:WP_075619342.1
          Length = 511

 Score =  481 bits (1238), Expect = e-140
 Identities = 256/527 (48%), Positives = 366/527 (69%), Gaps = 24/527 (4%)

Query: 18  NPILNISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFL 77
           NP++ I +F++ + +T+ +     K T+ +++FYT G   SG QNGLAI+GDYLSAASFL
Sbjct: 2   NPVV-IILFLIIVGMTLAITYFAAKKTNTASEFYTAGGGLSGWQNGLAISGDYLSAASFL 60

Query: 78  GIVGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAA 137
           GI GAI+L G+DGFL+SIG+ VA+LV L +VAEPLRN+G++T+AD+++ R   K VR  A
Sbjct: 61  GIAGAIALYGFDGFLFSIGYLVAYLVVLFIVAEPLRNLGKYTLADMINSRFNAKKVRAGA 120

Query: 138 ACGTLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTY 197
           A  ++ + +FY+IAQ+ GAG+L+ +L DI    W AV+  +VGI+M  YVL GGM  T++
Sbjct: 121 ALSSITIVIFYMIAQLVGAGALIQLLFDIPY--WVAVL--LVGIMMTIYVLFGGMTATSW 176

Query: 198 VQMIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGL 257
           VQ+IKAVLL+ G  I++ L   K +  +       +E       A   G D    L PG+
Sbjct: 177 VQIIKAVLLMAGTMIISFLVLAKFNFNI-------MEMFTFMKTATPHGAD---YLNPGV 226

Query: 258 QYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMT 317
           +Y       LD +SL +AL LGTAGLPH+LMRF+TV  AK AR SV WA  ++G FY+MT
Sbjct: 227 KY----KVPLDTLSLMIALVLGTAGLPHILMRFFTVRDAKTARSSVMWATWIVGIFYVMT 282

Query: 318 LVLGYGAAALVGPDRVIAAPGAANAAAPLLAFELGGSIFMALISAVAFATVLAVVAGLAI 377
           + LG+GAAA VG D +++   A N AAPLLA  LGG + M+ +SAVAFAT+LAVVAGL +
Sbjct: 283 IFLGFGAAAFVGQDLIVSTNPAGNMAAPLLAQALGGDLLMSFVSAVAFATILAVVAGLVL 342

Query: 378 TASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLVALAF 437
           + ++A  HDIY  +I+ G++TE +Q+  +R   V + + SI+L + A + NVAFLV+LAF
Sbjct: 343 SGASAFAHDIYGQIIKKGKATEKQQMNAARYASVGVAVFSIILALGAQSLNVAFLVSLAF 402

Query: 438 AVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSG--NDSAMVPGAD 495
            +AASANLP I+Y+++WKKFNT GA++++ TGL+SAL+L+ +SP+V      +A++ G  
Sbjct: 403 CIAASANLPVIVYTIFWKKFNTAGALSSMITGLVSALILVSISPSVMNPVEGAALITGN- 461

Query: 496 WAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAEMEVRSLTG 542
             IFPL NP L+S+PL F+ GWIGT++ K  N +   AE++V++ TG
Sbjct: 462 -PIFPLTNPALLSVPLGFLGGWIGTMLTKEVN-EAKFAEVKVKANTG 506


Lambda     K      H
   0.324    0.138    0.393 

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: 654
Number of extensions: 34
Number of successful extensions: 4
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: 551
Length of database: 511
Length adjustment: 35
Effective length of query: 516
Effective length of database: 476
Effective search space:   245616
Effective search space used:   245616
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 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