GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglA in Herbaspirillum seropedicae SmR1

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate HSERO_RS22465 HSERO_RS22465 sugar ABC transporter

Query= TCDB::O05176
         (512 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS22465 HSERO_RS22465 sugar ABC
           transporter
          Length = 518

 Score =  435 bits (1118), Expect = e-126
 Identities = 232/505 (45%), Positives = 338/505 (66%), Gaps = 5/505 (0%)

Query: 1   MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTY 60
           M+  +LEM+ I K+F GV+AL  +++K++ GE   L GENGAGKSTLMK+LSGVYP GT+
Sbjct: 1   MSEYLLEMKGIVKSFGGVRALNGIDIKIRPGECVGLCGENGAGKSTLMKILSGVYPHGTW 60

Query: 61  EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVA-SNGVISWQQ 119
           EGEI ++G      ++ D+E  GI+IIHQEL LVP LS+AENIF+G+E+    G +++  
Sbjct: 61  EGEILWDGKPLQAHSVRDTEAAGIVIIHQELMLVPELSVAENIFMGHEITLPGGRMNYPA 120

Query: 120 TFNRTRELLKKVGLKESPETL-ITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESD 178
            + R  EL++++ + +    L ++  G G QQLVEIAKAL+K  +LLILDEP++SL  S+
Sbjct: 121 MYRRAEELMRELNMPDINVALPVSQYGGGHQQLVEIAKALNKDARLLILDEPSSSLTASE 180

Query: 179 SEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVII 238
              LL ++ + + +G+  + I+HKL+EV +V D I+V+RDG  + T     +E+  D II
Sbjct: 181 IGVLLKIIKDLKARGVACVYISHKLDEVAEVCDTISVIRDGKHIATTP--MQEMDVDKII 238

Query: 239 RNMVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGL 298
             MVGR++   YP R+  IGE +LE +N   Y   +  R+ + D++ +VR+GE++GIAGL
Sbjct: 239 TQMVGREITAMYPERNHAIGEVVLEARNITCYDIDNPRRKRVDDVSFSVRRGEILGIAGL 298

Query: 299 MGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLN 358
           +GAGRTE   ++FG +Y  R  G VL++GKP D S+  K+I  GL  V EDRKH G+V +
Sbjct: 299 VGAGRTELVSAIFG-AYRGRYEGQVLLEGKPADTSSPLKSIRRGLCMVPEDRKHHGIVPD 357

Query: 359 DNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVV 418
            ++  N TL  L   S+ S ID   E+K   D   R+R++++  F    +LSGGNQQK V
Sbjct: 358 LDVGQNITLTVLNRFSRGSRIDGSAELKTIQDEIGRMRVKTATPFLPITSLSGGNQQKAV 417

Query: 419 LSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRI 478
           L+K L + P VLILDEPTRG+DVGAK EIY +I++LA  G  ++M+SSE+ E+LG  DR+
Sbjct: 418 LAKMLLAQPKVLILDEPTRGVDVGAKAEIYRLISELAKAGLAIIMVSSELAEVLGVSDRV 477

Query: 479 YVMNEGRIVAELPKGEASQESIMRA 503
            V+ EGR+  +      SQE+++ A
Sbjct: 478 LVIGEGRLRGDFVNDNLSQETVLAA 502


Lambda     K      H
   0.316    0.135    0.374 

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: 653
Number of extensions: 34
Number of successful extensions: 9
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: 512
Length of database: 518
Length adjustment: 35
Effective length of query: 477
Effective length of database: 483
Effective search space:   230391
Effective search space used:   230391
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 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 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