GapMind for catabolism of small carbon sources

 

Alignments 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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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