GapMind for catabolism of small carbon sources

 

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

Align Acetate transporter (characterized, see rationale)
to candidate WP_011386681.1 AMB_RS21920 cation acetate symporter

Query= uniprot:G8AHY6
         (572 letters)



>NCBI__GCF_000009985.1:WP_011386681.1
          Length = 554

 Score =  697 bits (1800), Expect = 0.0
 Identities = 357/566 (63%), Positives = 440/566 (77%), Gaps = 17/566 (3%)

Query: 7   RVGVAAVAAGALIPASVHAAAVEGAVQKQATNFSAIVMFLVFVLATLGITYWAARRTKSA 66
           R+GV ++   A    ++ A A  G   +QATN+ AI+MF+ FVL TLGIT+WA++RTKSA
Sbjct: 6   RLGVLSLMLLAPSLPALAAGADLGQAARQATNWHAILMFVGFVLLTLGITWWASKRTKSA 65

Query: 67  KDFYAAGGGITGFQNGLAIAGDYMSAASFLGIAGLVYTSGFDGLIFSVGWLVGWPIILFL 126
            DFY AGGGITGFQNGLAIAGD+MSAASFLG+  L+Y +G DG++++VG +VGWP++LFL
Sbjct: 66  ADFYTAGGGITGFQNGLAIAGDFMSAASFLGVTALLYGTGLDGMVYAVGVVVGWPLMLFL 125

Query: 127 VAERLRNLGKYTFADVASYRFQQTPMRTMAACGSLATVTFYLIAQMVGAGKLIQLLFGMD 186
           +AE LRNLGKYTFADV +YR  + P+RT AA  SL  V FYLIAQMVGAG+LI+LLFGMD
Sbjct: 126 IAEPLRNLGKYTFADVVAYRLAKVPVRTYAAFSSLTVVVFYLIAQMVGAGQLIKLLFGMD 185

Query: 187 YLWAVVIVGVLMIAYVTFGGMLATTWVQIIKAVLLLSGASFMAFAVLAKFGFSPEAMFST 246
           YL+A+ +VG LM+ YVTFGGM ATTWVQIIKAVLLLSGA+FMA AVL++FGFSPEAMF+ 
Sbjct: 186 YLYALFLVGGLMMIYVTFGGMAATTWVQIIKAVLLLSGATFMAGAVLSRFGFSPEAMFAK 245

Query: 247 AVQVHPKATGIMAPGALITDPVSAISLGMALMFGTAGLPHILMRFFTVSDAKEARKSVFY 306
           AVQV   +  IM+PG L  DP+  ISL MAL FGTAGLPHILMRFFTV DAKEARKSVFY
Sbjct: 246 AVQV-KGSNAIMSPGLLFKDPIDTISLAMALAFGTAGLPHILMRFFTVPDAKEARKSVFY 304

Query: 307 ATGFIGYFYILTFIIGFGAIVLLLAPDATGAYPFLDAAKLAAAGGKPNPSMIIGGSNMAA 366
           AT FIG+FY+L  +IG GAI  L+A D T             A GK     + GG NMAA
Sbjct: 305 ATAFIGFFYVLAVVIGIGAIA-LVATDPT-----------YLADGK----ALKGGGNMAA 348

Query: 367 IHTAHAVGGDLFFGFISAVAFATILAVVAGLTLAGASAVSHDLYASVIAKGRASEHDEIR 426
           +  AHAVGGDLF GFISAVAFATILAVVAGLTLAGASA+SHDLYA+V A+G A E  E+R
Sbjct: 349 VWLAHAVGGDLFLGFISAVAFATILAVVAGLTLAGASAISHDLYANVFARGHAKEETELR 408

Query: 427 VSKITTVIIGIVSIFLGIAFENQNVAFMVGLAFVIAASANFPVLLMSMFWSRMTTRGAVL 486
           +S++ ++ +G+++I LG+ FE QN+A++ GL   IAASANFP+LL+SM W  +T+RGA+L
Sbjct: 409 ISRLASLALGVIAIILGMLFEKQNIAYLAGLTLAIAASANFPLLLLSMLWPGLTSRGAIL 468

Query: 487 GGWIGLVSSVSLLIMGPTVWKSVLGNPAALFPYDNPGVFTIPLSFLAIWFFSITDNSKAA 546
           GG  GLVS+V L ++GP VWK+VLGNP  +FP+ NP +F++   F A WFFS+TD S+ A
Sbjct: 469 GGVAGLVSAVVLTVLGPAVWKAVLGNPQPIFPWGNPALFSVAAGFAATWFFSVTDGSERA 528

Query: 547 QDEREAYKAQYIRSQTGLGAEGASAH 572
             E+  + AQ++RSQTGLGAEG SAH
Sbjct: 529 VREKAEFNAQFVRSQTGLGAEGVSAH 554


Lambda     K      H
   0.327    0.138    0.410 

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: 1102
Number of extensions: 61
Number of successful extensions: 4
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: 572
Length of database: 554
Length adjustment: 36
Effective length of query: 536
Effective length of database: 518
Effective search space:   277648
Effective search space used:   277648
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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