GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylG in Sinorhizobium meliloti 1021

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 SM_b20713 SM_b20713 sugar uptake ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>lcl|FitnessBrowser__Smeli:SM_b20713 SM_b20713 sugar uptake ABC
           transporter ATP-binding protein
          Length = 513

 Score =  439 bits (1128), Expect = e-127
 Identities = 234/491 (47%), Positives = 333/491 (67%), Gaps = 4/491 (0%)

Query: 4   ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63
           +L  + + K FPGV AL  V  +   G VHA++GENGAGKSTLMKI+AG+Y PD+GE+  
Sbjct: 23  LLTAEGVRKEFPGVVALDDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYPDQGEVKL 82

Query: 64  EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGI-FIDYKKMYREAE 122
            G G+R   P +A+  GI  + QEL++M  ++VAENI++  E K    F+D+ +M R   
Sbjct: 83  RGAGIRLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREPKNRFGFVDHGEMRRMTA 142

Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182
           K   E   I++DPE ++   S+A +QMVEIA+AV  ++ VLI+DEPTS+LT++E   LFE
Sbjct: 143 KLF-ERLKIDLDPEIEVRHLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVAHLFE 201

Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242
           +++ L+ +G+ I++I+H++ E+FEI D+ SV RDG+YIGT     +T++ I+ MMVGR++
Sbjct: 202 IIRDLRSQGIGIVYITHKMNELFEIADEFSVFRDGKYIGTHLSNEVTRDDIIRMMVGREI 261

Query: 243 EKFYIKEAHEPGEVVLEVKNLS-GERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGF 301
            + + KE    G+VVL VKNL+    F +VSF +R GEILG AGLVG+GR+ + ET+FG 
Sbjct: 262 TQMFPKEEVPIGDVVLSVKNLTLNGVFRDVSFDVRAGEILGVAGLVGSGRSNVAETLFGV 321

Query: 302 RPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSL-DRIK 360
            P   G I I+GK V I+    AI   +  + EDRK  G +LI+ I+ N+ +  L D+  
Sbjct: 322 TPASSGTIAIDGKEVVIDSANKAIRHRMAFLTEDRKDTGCLLILDILENMQIAVLQDKFV 381

Query: 361 KGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDE 420
           K  F+S +      +   +   ++      +V  LSGGNQQKV++ +WL   P+ILILDE
Sbjct: 382 KRGFVSEREVTAACEEMSRKLRVKTPNLQERVENLSGGNQQKVLIGRWLLTNPRILILDE 441

Query: 421 PTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKE 480
           PTRGIDVGAKAEI+R++++LA+ GV VIMISSE+PEVL MSDRI VM  G++ GI+D  E
Sbjct: 442 PTRGIDVGAKAEIHRLVTELARNGVAVIMISSEMPEVLGMSDRIMVMHEGRVTGILDRAE 501

Query: 481 ASQEKVMKLAA 491
           A+Q KVM+LAA
Sbjct: 502 ATQIKVMELAA 512



 Score =  103 bits (256), Expect = 2e-26
 Identities = 61/228 (26%), Positives = 121/228 (53%), Gaps = 9/228 (3%)

Query: 269 ENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQG 328
           ++V F L+RG +    G  GAG++ LM+ + G      GE+ + G  + +  PLDA+E G
Sbjct: 40  DDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYPDQGEVKLRGAGIRLKSPLDALENG 99

Query: 329 IGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAY- 387
           I ++ ++   L L+  M++  N+ +    + + G    F    E+     K F+      
Sbjct: 100 IAMIHQE---LNLMPFMTVAENIWIRREPKNRFG----FVDHGEMRRMTAKLFERLKIDL 152

Query: 388 -PDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVG 446
            P+ +V +LS  N+Q V +AK ++ +  +LI+DEPT  +     A ++ I+  L  +G+G
Sbjct: 153 DPEIEVRHLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVAHLFEIIRDLRSQGIG 212

Query: 447 VIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494
           ++ I+ ++ E+ +++D  +V   GK  G   + E +++ ++++  G E
Sbjct: 213 IVYITHKMNELFEIADEFSVFRDGKYIGTHLSNEVTRDDIIRMMVGRE 260


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: 682
Number of extensions: 37
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 494
Length of database: 513
Length adjustment: 34
Effective length of query: 460
Effective length of database: 479
Effective search space:   220340
Effective search space used:   220340
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 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