GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mctC in Azospirillum brasilense Sp245

Align Monocarboxylic acid transporter (characterized)
to candidate AZOBR_RS02940 AZOBR_RS02940 actetate permease

Query= SwissProt::Q8NS49
         (551 letters)



>FitnessBrowser__azobra:AZOBR_RS02940
          Length = 572

 Score =  439 bits (1130), Expect = e-127
 Identities = 247/556 (44%), Positives = 341/556 (61%), Gaps = 52/556 (9%)

Query: 23  ISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGA 82
           I +F+VF++ T+ +     + T  + DFY  G   +G QNGLAIAGDY+SAASFLGI G 
Sbjct: 42  IVMFLVFVLATLGITYWAARRTKSAKDFYAAGGGITGFQNGLAIAGDYMSAASFLGIAGL 101

Query: 83  ISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTL 142
           +  +G+DG ++S+G+ V W + L LVAE LRN+G++T ADV S+R +Q P+R  AACG+L
Sbjct: 102 VYTSGFDGLIFSVGWLVGWPIILFLVAERLRNLGKYTFADVASYRFQQTPMRTMAACGSL 161

Query: 143 AVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIK 202
           A   FYLIAQM GAG L+ +L  + ++ W  V   IVG++MIAYV  GGM  TT+VQ+IK
Sbjct: 162 ATVTFYLIAQMVGAGKLIQLLFGM-DYLWAVV---IVGVLMIAYVTFGGMLATTWVQIIK 217

Query: 203 AVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGLQYGAT 262
           AVLL+ G + M      K       + + AV+ H  +          T I+ P    GA 
Sbjct: 218 AVLLLSGASFMAFAVLAKFGFSPEAMFSTAVQVHPKA----------TGIMAP----GAL 263

Query: 263 LTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTLVLGY 322
           +T  +  ISL +AL  GTAGLPH+LMRF+TV  AKEARKSV +A   IG FY++T ++G+
Sbjct: 264 ITDPVSAISLGMALMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYILTFIIGF 323

Query: 323 GA-AALVGPDRVIAAP--------------------GAANAAAPLLAFELGGSIFMALIS 361
           GA   L+ PD   A P                    G +N AA   A  +GG +F   IS
Sbjct: 324 GAIVLLLAPDATGAYPFLDAAKLAAAGGKPNPSMIIGGSNMAAIHTAHAVGGDLFFGFIS 383

Query: 362 AVAFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLG 421
           AVAFAT+LAVVAGL +  ++AV HD+Y +VI  G+++E +++RVS+IT V+IG++SI LG
Sbjct: 384 AVAFATILAVVAGLTLAGASAVSHDLYASVIAKGRASEHDEIRVSKITTVIIGIVSIFLG 443

Query: 422 ILAMTQNVAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSP 481
           I    QNVAF+V LAF +AASAN P +L S++W +  T GAV   + GL+S++ L+ + P
Sbjct: 444 IAFENQNVAFMVGLAFVIAASANFPVLLMSMFWSRMTTRGAVLGGWIGLVSSVSLLIMGP 503

Query: 482 AVSGNDSAMVPGADWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAEME----- 536
            V  +    V G   A+FP  NPG+ +IPL+F+A W  ++    DN      E E     
Sbjct: 504 TVWKS----VLGNPAALFPYDNPGVFTIPLSFLAIWFFSIT---DNSKAAQDEREAYKAQ 556

Query: 537 -VRSLTGVGVEKAVDH 551
            +RS TG+G E A  H
Sbjct: 557 YIRSQTGLGAEGASAH 572


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: 734
Number of extensions: 33
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: 551
Length of database: 572
Length adjustment: 36
Effective length of query: 515
Effective length of database: 536
Effective search space:   276040
Effective search space used:   276040
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 17 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