GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Smeli:SM_b20713
          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.

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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