GapMind for catabolism of small carbon sources

 

Alignments for a candidate for actP in Thiohalospira halophila HL 3

Align Monocarboxylic acid transporter (characterized)
to candidate WP_093426893.1 BM272_RS00985 cation acetate symporter

Query= SwissProt::Q8NS49
         (551 letters)



>NCBI__GCF_900112605.1:WP_093426893.1
          Length = 604

 Score =  149 bits (376), Expect = 3e-40
 Identities = 92/304 (30%), Positives = 151/304 (49%), Gaps = 19/304 (6%)

Query: 27  VVFIIVTMTVVLRVG----KSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGA 82
           +++++V  T  L +G         + +FY  G       NG A A D++SAASF+ + G 
Sbjct: 6   LIYLVVGATFALYLGIAFWAKAGSTGEFYIAGGGVHPVANGAATAADWMSAASFISMAGL 65

Query: 83  ISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTL 142
           I+  GYDG +Y +G+   +++  LL+A  LR  G+FT+ + +  R      RV A    +
Sbjct: 66  IAFLGYDGSVYLMGWTGGYVLLALLLAPYLRKFGKFTVPEFIGDRYYSDTARVVAVICLI 125

Query: 143 AVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIK 202
            ++  Y+  QM G G + S  L++       + +G+V      Y +LGGMKG TY Q+ +
Sbjct: 126 FISFTYVAGQMRGVGIVFSRFLEVELLTGLIIGMGVV----FVYAVLGGMKGITYTQVAQ 181

Query: 203 AVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATK-----GYDPTQILEPGL 257
            V+++    +  V   ++V+G      N   +    +D A T        D T +     
Sbjct: 182 YVVMIFAYTVPAVFIALQVTG------NPIPQVALGADLAGTSTDLLAKLDQTLVDLGFG 235

Query: 258 QYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMT 317
            Y       +D   + LAL +GTAGLPHV++RF+TVP  ++AR+S  WA++ I   Y   
Sbjct: 236 PYTEGSKPTVDVFFITLALMVGTAGLPHVIVRFFTVPKVRDARRSAGWALLFIALLYTTA 295

Query: 318 LVLG 321
             +G
Sbjct: 296 PAVG 299



 Score = 66.6 bits (161), Expect = 3e-15
 Identities = 53/185 (28%), Positives = 88/185 (47%), Gaps = 7/185 (3%)

Query: 357 MALISAVAFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLI 416
           +AL++A   A  L+  AGL +  S+A+ HD+     R  Q +E  ++   RI      LI
Sbjct: 413 IALVAAGGVAAALSTAAGLLLVISSAISHDLLKRTFRP-QISERGELAAGRIAAATAILI 471

Query: 417 SIVLGILAMTQNVAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLL 476
           +  LG       VA +VA AF +AA++  P I+  ++ K+ N  GA+A +  GL+  L  
Sbjct: 472 AGYLGANPPAF-VAQVVAFAFGLAAASLFPVIIMGIFNKRMNREGAIAGMVVGLVFTLAY 530

Query: 477 IFLSPAVSGNDSAMVPGADWAIFPLKNPGL--VSIPLAFIAGWIGTLV--GKPDNMDDLA 532
           I     V     A     +W +F +   G+  +++ L F   W  + V    P ++ +L 
Sbjct: 531 IIYFKGVFVEPFAADVPENW-LFGISPEGIGGLAMLLNFAVAWTVSKVTAAPPQSIQELV 589

Query: 533 AEMEV 537
           A + V
Sbjct: 590 ASIRV 594


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: 710
Number of extensions: 43
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 551
Length of database: 604
Length adjustment: 36
Effective length of query: 515
Effective length of database: 568
Effective search space:   292520
Effective search space used:   292520
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: 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