GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mctC in Magnetospirillum magneticum AMB-1

Align Monocarboxylic acid transporter (characterized)
to candidate WP_011386681.1 AMB_RS21920 cation acetate symporter

Query= SwissProt::Q8NS49
         (551 letters)



>NCBI__GCF_000009985.1:WP_011386681.1
          Length = 554

 Score =  397 bits (1021), Expect = e-115
 Identities = 232/537 (43%), Positives = 319/537 (59%), Gaps = 31/537 (5%)

Query: 23  ISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGA 82
           I +FV F+++T+ +     K T  + DFYT G   +G QNGLAIAGD++SAASFLG+   
Sbjct: 41  ILMFVGFVLLTLGITWWASKRTKSAADFYTAGGGITGFQNGLAIAGDFMSAASFLGVTAL 100

Query: 83  ISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTL 142
           +   G DG +Y++G  V W + L L+AEPLRN+G++T ADV+++RL + PVR  AA  +L
Sbjct: 101 LYGTGLDGMVYAVGVVVGWPLMLFLIAEPLRNLGKYTFADVVAYRLAKVPVRTYAAFSSL 160

Query: 143 AVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIK 202
            V +FYLIAQM GAG L+ +L  + ++ +   +VG  G++MI YV  GGM  TT+VQ+IK
Sbjct: 161 TVVVFYLIAQMVGAGQLIKLLFGM-DYLYALFLVG--GLMMI-YVTFGGMAATTWVQIIK 216

Query: 203 AVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGLQYGAT 262
           AVLL+ G   M      +       +   AV+          KG     I+ PGL +   
Sbjct: 217 AVLLLSGATFMAGAVLSRFGFSPEAMFAKAVQ---------VKG--SNAIMSPGLLF--- 262

Query: 263 LTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTLVLGY 322
               +D ISLA+AL  GTAGLPH+LMRF+TVP AKEARKSV +A   IG FY++ +V+G 
Sbjct: 263 -KDPIDTISLAMALAFGTAGLPHILMRFFTVPDAKEARKSVFYATAFIGFFYVLAVVIGI 321

Query: 323 GAAALVGPDRVIAAPGAA-----NAAAPLLAFELGGSIFMALISAVAFATVLAVVAGLAI 377
           GA ALV  D    A G A     N AA  LA  +GG +F+  ISAVAFAT+LAVVAGL +
Sbjct: 322 GAIALVATDPTYLADGKALKGGGNMAAVWLAHAVGGDLFLGFISAVAFATILAVVAGLTL 381

Query: 378 TASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLVALAF 437
             ++A+ HD+Y  V   G + E  ++R+SR+  + +G+I+I+LG+L   QN+A+L  L  
Sbjct: 382 AGASAISHDLYANVFARGHAKEETELRISRLASLALGVIAIILGMLFEKQNIAYLAGLTL 441

Query: 438 AVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGNDSAMVPGADWA 497
           A+AASAN P +L S+ W    + GA+     GL+SA++L  L PAV       V G    
Sbjct: 442 AIAASANFPLLLLSMLWPGLTSRGAILGGVAGLVSAVVLTVLGPAV----WKAVLGNPQP 497

Query: 498 IFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAEME---VRSLTGVGVEKAVDH 551
           IFP  NP L S+   F A W  ++    +      AE     VRS TG+G E    H
Sbjct: 498 IFPWGNPALFSVAAGFAATWFFSVTDGSERAVREKAEFNAQFVRSQTGLGAEGVSAH 554


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: 700
Number of extensions: 32
Number of successful extensions: 7
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: 554
Length adjustment: 36
Effective length of query: 515
Effective length of database: 518
Effective search space:   266770
Effective search space used:   266770
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