GapMind for catabolism of small carbon sources

 

Alignments for a candidate for actP in Gracilibacillus halophilus YIM-C55.5

Align Acetate permease ActP-2/ActP2/ActP3 (characterized)
to candidate WP_003473551.1 J416_RS13350 cation acetate symporter

Query= TCDB::D5APM1
         (578 letters)



>NCBI__GCF_000359605.1:WP_003473551.1
          Length = 560

 Score =  195 bits (495), Expect = 5e-54
 Identities = 142/480 (29%), Positives = 230/480 (47%), Gaps = 52/480 (10%)

Query: 63  RTKSAADFYTAGGGITGFQNGLAIAGDYMSAASFLGISAAVMLQGYDGLIYSIGFLVGWP 122
           R +  ++FY AG G+    NG AIA D+MSAASF+ ++  V   GYDG IY +G+  G+ 
Sbjct: 26  RVRDTSNFYVAGQGVPTVANGAAIAADWMSAASFISMAGLVAFLGYDGTIYLMGWTGGYV 85

Query: 123 ILTFLMAERLRNLGKFTFADVAAFPFAQTPVRVFAAMSTLVVVAFYLIAQMVGAGQLIKL 182
           +L  L+A  LR  GKFT  D     F  +  R  AA++T+ +   Y+  QM G G +   
Sbjct: 86  LLALLLAPYLRKFGKFTVPDFIGDRFYSSTARSVAAIATIFISLTYISGQMRGVGIVFSR 145

Query: 183 LFGLEYLYAVIVVGILMMVYVLFGGMTATTWVQIIKACLLLGGASFMALMVMVHYGFSLE 242
              ++ +  V++   ++  + L GGM   TW Q I+  +++      A  +     F L 
Sbjct: 146 YLQVDIIIGVLIGMAIVGFFALLGGMKGVTWTQAIQYFVIIIAFLIPAFAI----SFQLT 201

Query: 243 SLFADSVKVKT-DLALAAGKTPEEAAAAGISIMGPGTFVKDPISAISFGMALMFGTAGLP 301
                 + + T D+    G+   E        M P T +   ++ +   +ALM GTAGLP
Sbjct: 202 GNPIPQLALTTSDIVDRLGQIQVELGMT--EYMAPFTDL-SMLNVLMMTLALMAGTAGLP 258

Query: 302 HILMRFFTVPSAKEARKSVMWATVWIGYFYMLTFIIG----FGAIVYVLTNP-------- 349
           H+++RF+TV S + AR S +WA V+IG  Y+    +G    +  I  +   P        
Sbjct: 259 HVIVRFYTVKSVRAARWSAVWAIVFIGLLYVTAPAVGAFAKYNLIDTIADKPIEEVQDID 318

Query: 350 GLVSYDAKGALTLVGGNNMAAIHLA------QAVGGNI--------------FLGFISAV 389
            +  ++  G L L   N    ++          + G+I               +  ++A 
Sbjct: 319 WVNKWETTGLLQLDDANGDGIVNFTGDDQNEVMIDGDIIVLSTPEVANLAPFIIALVAAG 378

Query: 390 AFATILAVVAGLTLSGASAVSHDLYSTVFKNGKADSASELRVSRITTICLGIVAVVLGL- 448
             A  L+  +GL ++  SAVSHD+Y  +F N KA  A  LRV RIT     ++A  +G+ 
Sbjct: 379 GLAAALSTASGLLITMTSAVSHDIYYRIF-NKKASEAQRLRVGRITLFVALLIAAYVGIN 437

Query: 449 --AFEKQNIAFMVSLAFAIAASANFPVLFMSLLWKGMTTRGAVIGGSLGLISSVALTVIS 506
              F  +    +V+LAF + A++ FPV+ + +  K M   GAV     G+I+ ++ T+I+
Sbjct: 438 PPGFAGE----VVALAFGLGAASLFPVILLGIFDKRMNKEGAV----AGIITGLSFTLIT 489


Lambda     K      H
   0.326    0.138    0.405 

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: 898
Number of extensions: 53
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: 578
Length of database: 560
Length adjustment: 36
Effective length of query: 542
Effective length of database: 524
Effective search space:   284008
Effective search space used:   284008
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 (21.7 bits)
S2: 53 (25.0 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