GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Acidovorax sp. GW101-3H11

Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate Ac3H11_607 Predicted L-arabinose ABC transport system, ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_607
          Length = 517

 Score =  363 bits (931), Expect = e-104
 Identities = 195/499 (39%), Positives = 314/499 (62%), Gaps = 12/499 (2%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           P+L++  IHK+F G+  L+ V +  YPGE+HA++G+NGAGKSTL+K++ GV +   G++ 
Sbjct: 17  PVLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMR 76

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIF----IDYKKMY 118
             G+ V  + P  A   GI TV+QE+++  NLSVAENIF G   + GI     ID+  ++
Sbjct: 77  LGGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYPRCGIAQGFRIDWATLH 136

Query: 119 REAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETE 178
           + A   +    G++ID    L  Y +A+QQ+V IARA+  +++VLILDEPTSSL   E +
Sbjct: 137 QRARDLVAR-IGLQIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDDEVQ 195

Query: 179 KLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMV 238
           KLFEV++ L+ +G++I+F++H L +++ + D+++VLR+G ++G    ++L  + ++  M+
Sbjct: 196 KLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGPQALIAAML 255

Query: 239 GRKLEKFYIKEAHEPGEVVLEVKNLSGE------RFENVSFSLRRGEILGFAGLVGAGRT 292
           GR L     + A  P         L  E      + + +   +R GE++G AGL+G+GRT
Sbjct: 256 GRDLAAASEQPAPAPAVDSRHANLLQAEGLGQDTQLQPLDLQIRAGEVVGLAGLLGSGRT 315

Query: 293 ELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVS 352
           EL   +FG      G + I+G+ V+  +P+DAI  G+ L PE+RK  G++  +S+  N++
Sbjct: 316 ELARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLALCPEERKTDGIVAELSVRENIA 375

Query: 353 LPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALK 412
           L    R+  G F+S   + ELA+  +K   I+    D+ +  LSGGNQQK +LA+W+A++
Sbjct: 376 LALQARMGVGKFLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGNQQKAILARWMAIE 435

Query: 413 PKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKL 472
           P++LILDEPTRGIDV AK EI   + +LA+ G+ V+ ISSE+ EV++++ RI V+   + 
Sbjct: 436 PRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRVAHRIVVLRDRRK 495

Query: 473 AGIIDAKEASQEKVMKLAA 491
            G + A  +S++ V  L A
Sbjct: 496 VGELPA-GSSEDAVYDLIA 513



 Score = 77.0 bits (188), Expect = 1e-18
 Identities = 61/229 (26%), Positives = 111/229 (48%), Gaps = 14/229 (6%)

Query: 270 NVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGI 329
           +V  +L  GEI    G  GAG++ L++ + G     GG++ + G+ V  + PL A   GI
Sbjct: 36  DVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMRLGGQAVWPDSPLAAQRLGI 95

Query: 330 GLVPEDRKKLGLILIMSIMHNVSLPSLDR--IKKGPFISF----KREKELADWAIKTFDI 383
             V ++   + L   +S+  N+      R  I +G  I +    +R ++L        D+
Sbjct: 96  STVYQE---VNLCPNLSVAENIFAGRYPRCGIAQGFRIDWATLHQRARDLVARIGLQIDV 152

Query: 384 RPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKE 443
                D  V       QQ V +A+ L+++ ++LILDEPT  +D     +++ ++ +L  E
Sbjct: 153 TRLLSDYPVAV-----QQLVAIARALSIESRVLILDEPTSSLDDDEVQKLFEVLRRLRSE 207

Query: 444 GVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAG 492
           G+ ++ ++  L +V  +SDRI V+  G   G   AK+   + ++    G
Sbjct: 208 GLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGPQALIAAMLG 256


Lambda     K      H
   0.318    0.138    0.385 

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: 610
Number of extensions: 22
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 494
Length of database: 517
Length adjustment: 34
Effective length of query: 460
Effective length of database: 483
Effective search space:   222180
Effective search space used:   222180
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 (21.7 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:

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