GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Dinoroseobacter shibae DFL-12

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 3607108 Dshi_0530 ABC transporter related (RefSeq)

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__Dino:3607108
          Length = 498

 Score =  322 bits (826), Expect = 1e-92
 Identities = 180/480 (37%), Positives = 286/480 (59%), Gaps = 6/480 (1%)

Query: 5   LEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYE 64
           +++++I KR+ GV AL  V     PGE   + GENG+GKSTL+KII+GV     G +   
Sbjct: 10  IDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIA 69

Query: 65  GRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKF 124
           G+     +P  +  AG++ +FQ+ S+  NLSVAENI    +      +   +  R+  + 
Sbjct: 70  GQEHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRDIARA 129

Query: 125 MKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVV 184
             +  G++ID + ++    +A +Q+V I RA+  KA+++I+DEPT++LT+KE  +L  ++
Sbjct: 130 ALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQGII 189

Query: 185 KSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLEK 244
           + LKE+GVA+IF+SH+L E+ E+ +KV VLR+G+ +          + +   M GR + +
Sbjct: 190 RMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYHMTGRDVPE 249

Query: 245 FYIKEAHEPGEVVLEVKNLS-GERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRP 303
               +     + +++V+ L     F ++SF LR GE+LG  GL+G GRT + + +FG   
Sbjct: 250 VPPSDVAAGAQTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLLGCGRTSVAKALFGLVT 309

Query: 304 KRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGP 363
              G I ++G  V +  P  A    IG VPEDR   GL L  SI+ NV++  LD    G 
Sbjct: 310 PDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVGRLDAHTSGG 369

Query: 364 FISFKR-EKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPT 422
           F+      KE +DW ++   ++    +  V  LSGGNQQ+V LA+WL+  P++LIL+ P+
Sbjct: 370 FLDMTGLAKEASDW-LRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAPRVLILNGPS 428

Query: 423 RGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEAS 482
            G+DVG+KA+I+ I+ +LA+EG+GVI+IS +LPE+L    R+ VM  G+   IIDA E +
Sbjct: 429 VGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGR---IIDALEGT 485



 Score = 82.0 bits (201), Expect = 4e-20
 Identities = 58/220 (26%), Positives = 105/220 (47%), Gaps = 5/220 (2%)

Query: 23  VSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAINAGIV 82
           +S +   GEV  I G  G G++++ K + G+  PD G I+ +G  V    P  A  A I 
Sbjct: 277 ISFDLRTGEVLGITGLLGCGRTSVAKALFGLVTPDAGSILVDGSPVPLGDPQAASLARIG 336

Query: 83  TVFQEL---SVMDNLSVAENIFMG--DEEKRGIFIDYKKMYREAEKFMKEEFGIEIDPEE 137
            V ++     +  + S+  N+ +G  D    G F+D   + +EA  +++       D E 
Sbjct: 337 YVPEDRLTEGLFLSQSILRNVAVGRLDAHTSGGFLDMTGLAKEASDWLRRLKVKAPDVEA 396

Query: 138 KLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGVAIIFI 197
            +   S   QQ V +AR + +  +VLIL+ P+  +       + ++++ L  +G+ +I I
Sbjct: 397 PVQSLSGGNQQRVALARWLSRAPRVLILNGPSVGVDVGSKADIHDIIRELAREGIGVIVI 456

Query: 198 SHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMM 237
           S  L E+   C +V V+R+G  I       LT++ +   +
Sbjct: 457 SDDLPELLATCHRVLVMREGRIIDALEGTALTEDDLAHRL 496


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: 538
Number of extensions: 22
Number of successful extensions: 6
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: 498
Length adjustment: 34
Effective length of query: 460
Effective length of database: 464
Effective search space:   213440
Effective search space used:   213440
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