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

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|NCBI__GCF_000009985.1:WP_011386681.1 AMB_RS21920 cation acetate
           symporter
          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.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources