GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acaP in Lactobacillus shenzhenensis LY-73

Align Aspartate/Glutamate transporter of 488 aas and 12 TMSs, AcaP (characterized)
to candidate WP_022528465.1 L248_RS02440 APC family permease

Query= TCDB::F2HJG8
         (488 letters)



>NCBI__GCF_000469325.1:WP_022528465.1
          Length = 554

 Score =  328 bits (842), Expect = 2e-94
 Identities = 168/483 (34%), Positives = 283/483 (58%), Gaps = 19/483 (3%)

Query: 6   IRWFTVAFIAFNMVWGMGNVVNNFAQQGITVVTSWLLILALYFIPYALIVGQLGSTFKDS 65
           I W  VA + F  V G  +++ NF  QG+  VTSW+L+  LY IPY+LIV  LGSTF   
Sbjct: 12  IPWVVVALMDFVTVIGFDDIIYNFRNQGLVAVTSWVLMTFLYVIPYSLIVAHLGSTFSAD 71

Query: 66  KGGVSSWVENTSTKRLAYYAAWTYWVVHIPYLAQKPQAILIAFGWVGQGNGNLVSQMSMT 125
            GG++SWV  T+   L Y+AAW YW+  +PY+     +++I+FGW+  G+G++ S M+  
Sbjct: 72  AGGITSWVRETNGDTLGYFAAWFYWITGLPYVVDVANSVVISFGWMVNGDGDIQSHMNNA 131

Query: 126 AVALISLAIFLAFLWLSTKGLS-TLKVIGGLAGTAMFVMSLLFIVMAI-----GAPFIAK 179
              L++  +F+ F+W  ++  + +L+++  + G AMF+M++LF+ M I     G+P   +
Sbjct: 132 WFGLLTAVVFIFFIWFQSRFQNKSLEIMSVIGGGAMFIMTVLFVGMTIVGLTQGSPIKTQ 191

Query: 180 DFHIATPDMGNIKTYIP-KFDFSYFTTISMLVFAVGGAEKISPYVNQTKNPAKEFPRGMF 238
            F        N++ ++P K D S+F T  + +FA+ G+E  +PY    K+P+++FP+ + 
Sbjct: 192 PF--------NLQAFLPKKLDLSFFATFGLFIFAMNGSELAAPYTADMKHPSRDFPKSLK 243

Query: 239 LLAGMVGICAVLGSIAMGMIFSSGNLPNDLMANGAYAAFQILGQHFGVGNFLMIVYALTN 298
           ++A M     + G+ ++G+ F++ +LPNDL  NG+Y AFQ +G+ FG+GN LM V+A+  
Sbjct: 244 MIAVMTMFLTLFGTFSLGVYFNAHHLPNDLKMNGSYYAFQAIGKQFGLGNILMYVFAVVQ 303

Query: 299 GVGQIAALAFSIDAPLLILLADADPEFVSAWLRKKTNKGTLKNGYTLTGILVSIIILLPL 358
            +  +A LA  +DA   + L D    F+   L K    G   NGY +T IL  II+++  
Sbjct: 304 CIYMLAQLAVILDASTRVFLGDMAKRFMPRQLSKTNAAGLPINGYWMTTILCGIIMVIAG 363

Query: 359 LGIGDMNELVKWLTNLNSVVMPMRYLWVFFAFIMLNRAVKHFQS-EYKFIKQKRLAMIAG 417
             +  +N++  WL NLN +V P    ++F+AF+M+ R    + +  Y ++K  R+  + G
Sbjct: 364 F-LPQINDIFNWLLNLNGIVSPFSTCFLFWAFMMVRRHSDRYPTPSYTYLKNDRVGFLVG 422

Query: 418 AWCFLFTLIACVLGMVPKLDYAANPSAWWFQLASNILTPIVLILLGMLLPFIARREQRKT 477
            W F  T +  ++G  P +D A   + W   L   I+  + +++LG L+P+IA+R QR+ 
Sbjct: 423 LWMFAITFLFALMGFWP-VDAAYGSALWTRSLVLYIVVTLGMVVLGFLMPWIAKR-QRER 480

Query: 478 NGL 480
           +GL
Sbjct: 481 DGL 483


Lambda     K      H
   0.327    0.140    0.435 

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: 802
Number of extensions: 43
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: 488
Length of database: 554
Length adjustment: 35
Effective length of query: 453
Effective length of database: 519
Effective search space:   235107
Effective search space used:   235107
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 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