GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__HerbieS:HSERO_RS22465
          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.

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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