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 Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized)
to candidate WP_011385006.1 AMB_RS13215 cation acetate symporter

Query= SwissProt::P32705
         (549 letters)



>NCBI__GCF_000009985.1:WP_011385006.1
          Length = 554

 Score =  658 bits (1697), Expect = 0.0
 Identities = 328/554 (59%), Positives = 421/554 (75%), Gaps = 5/554 (0%)

Query: 1   MKRVLTALAA-TLPFAANAADAISGAVERQPTNWQAIIMFLIFVVFTLGITYWASKRVRS 59
           MKR+L  L A  +P AA A     G  E+QP N  AI MF  FV+ TLGITYWASKR +S
Sbjct: 1   MKRILPILLALAVPTAALAGPGDLGGSEKQPINVTAIAMFFAFVMGTLGITYWASKRTKS 60

Query: 60  RSDYYTAGGNITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSLGFLVGWPIILF 119
            SD+YTAGG ITGFQNGLAIAGDYMSAA+ LG+S++VF +G+DG IY++ F VGWPIILF
Sbjct: 61  ASDFYTAGGGITGFQNGLAIAGDYMSAATLLGLSSMVFATGFDGFIYTISFFVGWPIILF 120

Query: 120 LIAERLRNLGRYTFADVASYRLKQGPIRILSACGSLVVVALYLIAQMVGAGKLIELLFGL 179
           L+AERLRNLGRYTFAD+ASYRL Q  +R  +A GSL VV  YLI QMVGAG+LI+LLFGL
Sbjct: 121 LLAERLRNLGRYTFADIASYRLDQSKVRTFAAMGSLTVVCFYLIVQMVGAGQLIKLLFGL 180

Query: 180 NYHIAVVLVGVLMMMYVLFGGMLATTWVQIIKAVLLLFGASFMAFMVMKHVGFSFNNLFS 239
           +Y +AV++VGVLM++YV FGGM+ATTWVQIIKA LLL G   +  + +   GFS  N+ +
Sbjct: 181 DYAVAVIIVGVLMVVYVTFGGMIATTWVQIIKACLLLGGGVLLCALALSKFGFSLENVAA 240

Query: 240 EAMAVHPKGVDIMKPGGLVKDPISALSLGLGLMFGTAGLPHILMRFFTVSDAREARKSVF 299
           +A+  H  GV IM PG ++ DP+SA+SL LGL+FGTA LPHILMRFFTV +A+EARKSVF
Sbjct: 241 KAVESHKAGVKIMGPGTMLADPVSAVSLSLGLVFGTAALPHILMRFFTVPNAKEARKSVF 300

Query: 300 YATGFMGYFYILTFIIGFGAIMLVGANPEYKD---AAGHLIGGNNMAAVHLANAVGGNLF 356
            A+GF+G+F+++  I+G  A+ +VG +P++ +     G L+GG NM  +HLA A+GG++F
Sbjct: 301 VASGFIGFFFLIVCILGLAAVSIVGTDPQFFEGGKVGGKLLGGGNMPVMHLAKALGGDIF 360

Query: 357 LGFISAVAFATILAVVAGLTLAGASAVSHDLYANVFKKG-ATEREELRVSKITVLILGVI 415
           LGF+SAVAFATILAVV+GL LAGASA++HD+YA V +KG ATE EE+RVSK++ L+LGV+
Sbjct: 361 LGFLSAVAFATILAVVSGLALAGASAIAHDIYARVIRKGHATEAEEMRVSKLSSLVLGVV 420

Query: 416 AIILGVLFENQNIAFMVGLAFAIAASCNFPIILLSMYWSKLTTRGAMMGGWLGLITAVVL 475
           A+ILG++FE QN+AF+VGL F IAAS NFP++ LSMYW  LTT+GA+ GG  GL++AV  
Sbjct: 421 AVILGIMFEKQNVAFLVGLTFGIAASANFPVLFLSMYWRGLTTKGALWGGIAGLVSAVTC 480

Query: 476 MILGPTIWVQILGHEKAIFPYEYPALFSITVAFLGIWFFSATDNSAEGARERELFRAQFI 535
           ++L   +WV +L +   IFPYE+PALFS+T+AFL     S  D S     E+ LF  Q++
Sbjct: 481 VVLSKAVWVVVLNNPAPIFPYEHPALFSMTLAFLVTIVVSKLDGSETAKAEKALFDDQYV 540

Query: 536 RSQTGFGVEQGRAH 549
           R+QTG G      H
Sbjct: 541 RAQTGIGAASASNH 554


Lambda     K      H
   0.329    0.142    0.424 

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: 938
Number of extensions: 47
Number of successful extensions: 3
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: 549
Length of database: 554
Length adjustment: 36
Effective length of query: 513
Effective length of database: 518
Effective search space:   265734
Effective search space used:   265734
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 (21.8 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