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

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_011383956.1 AMB_RS07815 cation acetate symporter

Query= uniprot:G8AHY6
         (572 letters)



>NCBI__GCF_000009985.1:WP_011383956.1
          Length = 561

 Score =  735 bits (1898), Expect = 0.0
 Identities = 375/557 (67%), Positives = 448/557 (80%), Gaps = 17/557 (3%)

Query: 18  LIPASVHAAAVEGAVQKQATNFSAIVMFLVFVLATLGITYWAARRTKSAKDFYAAGGGIT 77
           L  A++ A A  G  +KQATN+ AI+MF++FV ATLGITYWAA RTK+A DFYAAGGGIT
Sbjct: 20  LASAALAAGADMGGAEKQATNWHAIIMFVIFVGATLGITYWAAGRTKTAADFYAAGGGIT 79

Query: 78  GFQNGLAIAGDYMSAASFLGIAGLVYTSGFDGLIFSVGWLVGWPIILFLVAERLRNLGKY 137
           GFQNGLAIAGDYMSAASFLGI+ LVY SG+DGLIFSVGWLVGWPIILFL+AERLRNLGKY
Sbjct: 80  GFQNGLAIAGDYMSAASFLGISALVYGSGYDGLIFSVGWLVGWPIILFLIAERLRNLGKY 139

Query: 138 TFADVASYRFQQTPMRTMAACGSLATVTFYLIAQMVGAGKLIQLLFGMDYLWAVVIVGVL 197
           TFADV  YR  +TP+RT AA GSL  V FYLI QMVGAG+LI+LLFGMDY++AV+IVG L
Sbjct: 140 TFADVCGYRLARTPIRTFAATGSLIVVIFYLIGQMVGAGQLIKLLFGMDYVYAVMIVGAL 199

Query: 198 MIAYVTFGGMLATTWVQIIKAVLLLSGASFMAFAVLAKFGFSPEAMFSTAVQVHPKATGI 257
           M+ YVTFGGM+ATTWVQIIKA LLL GA+F+AF V+++FGFS E +F  A++VHPK   I
Sbjct: 200 MMVYVTFGGMVATTWVQIIKACLLLGGATFIAFGVMSQFGFSFEKLFVKAIEVHPKKVAI 259

Query: 258 MAPGALITDPVSAISLGMALMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYIL 317
           MAPGAL+T+PV AISLGMALMFGTAGLPHILMRFFTV DA+EARKSVFYATGFIGYFYIL
Sbjct: 260 MAPGALVTNPVDAISLGMALMFGTAGLPHILMRFFTVPDAREARKSVFYATGFIGYFYIL 319

Query: 318 TFIIGFGAIVLLLA-PD-ATGAYPFLDAAKLAAAGGKPNPSMIIGGSNMAAIHTAHAVGG 375
           TFIIGFGAI ++   P+  T     LD               + GG+NMAA+  AHA+GG
Sbjct: 320 TFIIGFGAITMVATNPEYLTKGLGSLD---------------LKGGNNMAAVWLAHAIGG 364

Query: 376 DLFFGFISAVAFATILAVVAGLTLAGASAVSHDLYASVIAKGRASEHDEIRVSKITTVII 435
           +LF GFISAVAFATILAVV+GLTLAGASA+SHDLYASVI  G+A+E  E+ VSKI ++ +
Sbjct: 365 NLFLGFISAVAFATILAVVSGLTLAGASAISHDLYASVIMHGQATEGKEVTVSKIASICL 424

Query: 436 GIVSIFLGIAFENQNVAFMVGLAFVIAASANFPVLLMSMFWSRMTTRGAVLGGWIGLVSS 495
           G++++ LG+ FE QNVAF+V L F +AASANFPVL++SMFW  +TTRGAVLGG IGL+ S
Sbjct: 425 GVIAVLLGLVFEKQNVAFIVALTFSVAASANFPVLVLSMFWGGLTTRGAVLGGMIGLLMS 484

Query: 496 VSLLIMGPTVWKSVLGNPAALFPYDNPGVFTIPLSFLAIWFFSITDNSKAAQDEREAYKA 555
           V ++++   VW    G  A +FP+  P +F++P +F   W FSI DNS +AQ ER AY+A
Sbjct: 485 VIMVVLSKAVWVQSFGFKAEIFPFAYPALFSVPAAFFFSWLFSIMDNSPSAQAERAAYEA 544

Query: 556 QYIRSQTGLGAEGASAH 572
           Q IRS+TGLGAEGA++H
Sbjct: 545 QSIRSETGLGAEGAASH 561


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: 1144
Number of extensions: 63
Number of successful extensions: 2
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: 561
Length adjustment: 36
Effective length of query: 536
Effective length of database: 525
Effective search space:   281400
Effective search space used:   281400
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
the source code
instructions for running GapMind on your computer

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