Alignments for a candidate for mglA in Tistlia consotensis USBA 355

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Tistlia consotensis USBA 355

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 WP_085120648.1 B9O00_RS01470 sugar ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>NCBI__GCF_900177295.1:WP_085120648.1
          Length = 634

 Score =  348 bits (893), Expect = e-100
 Identities = 197/497 (39%), Positives = 300/497 (60%), Gaps = 12/497 (2%)

Query: 4   ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63
           IL    I K F    AL G  +E   GEVH ++G NGAGKSTL K+I+G  Q D G ++Y
Sbjct: 14  ILVASGIEKTFDRTRALAGADLELRAGEVHGLLGANGAGKSTLSKVISGHVQRDAGRLVY 73

Query: 64  EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEK 123
           +GR +      EA+ AGI  V QE S+  +LSV ENIF+ +  + G+ + Y  M R A  
Sbjct: 74  KGRPLALRSTREALEAGIAIVMQETSLAPDLSVLENIFLPELGRPGL-LSYGSMRRRAVG 132

Query: 124 FMKEEFGIEIDP-EEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182
            +       + P + ++ + S A +Q+VEIA+A+   A ++I DEPT+SL+  E E+LF+
Sbjct: 133 LLANLGHEHVLPLDREVARLSAAQRQLVEIAKALALDADLIIFDEPTASLSPSEVERLFD 192

Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDS-IENLTKEKIVEMMVGRK 241
           ++  L++ G A+IF+SHRLEE+F I D+V+++R+G  +       +LT+ +++  MVGR 
Sbjct: 193 IMAKLRDDGRALIFVSHRLEEVFAITDRVTIMREGATVAASQPTASLTQAEVIRHMVGRD 252

Query: 242 LEKFY----IKEAHEPGEVVLEVKNLSGE-RFENVSFSLRRGEILGFAGLVGAGRTELME 296
           +   Y    ++E  E    V  V+NL+      NVSF +RRGEILG  GLVGAGR+E  E
Sbjct: 253 IGALYATPGLQEEDERAPAVFSVENLAAPPAVRNVSFFVRRGEILGLGGLVGAGRSETAE 312

Query: 297 TIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSL 356
            IFG RP+  G I +EG+ +    P DA+  GIG V EDR+   ++  +S+  N+ L  L
Sbjct: 313 AIFGLRPRSAGTIRLEGREIAPRKPADAVRAGIGFVAEDRRVQNIVPDLSVKENLLLAHL 372

Query: 357 DRIKKGPFISFKREKELADWAIKTFDIRPAYP--DRKVLYLSGGNQQKVVLAKWLALKPK 414
               +G  + ++R ++  +  +    + PA    D  +L  SGG QQK+++A+WL L+PK
Sbjct: 373 GA-HRGFGLGYRRRRQKVEELMAALGL-PAERLLDANMLNFSGGMQQKIIIARWLLLEPK 430

Query: 415 ILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAG 474
           +LILDEPT+G+D+G +  IY I+ ++A EGV V++ISS+  E+L + +R+ VMS G    
Sbjct: 431 VLILDEPTKGVDIGTRQAIYGILRRIADEGVAVVVISSDFEELLGVCERVVVMSDGNAIA 490

Query: 475 IIDAKEASQEKVMKLAA 491
            + +    +EK+  LAA
Sbjct: 491 DLPSALLDEEKLTLLAA 507



 Score = 97.1 bits (240), Expect = 2e-24
 Identities = 67/228 (29%), Positives = 119/228 (52%), Gaps = 7/228 (3%)

Query: 19  ALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAIN 78
           A++ VS     GE+  + G  GAG+S   + I G+     G I  EGR +    P++A+ 
Sbjct: 283 AVRNVSFFVRRGEILGLGGLVGAGRSETAEAIFGLRPRSAGTIRLEGREIAPRKPADAVR 342

Query: 79  AGIVTVFQELSVMD---NLSVAENIFMGD-EEKRGIFIDYKKMYREAEKFMKEEFGIEID 134
           AGI  V ++  V +   +LSV EN+ +      RG  + Y++  ++ E+ M    G+  +
Sbjct: 343 AGIGFVAEDRRVQNIVPDLSVKENLLLAHLGAHRGFGLGYRRRRQKVEELMAA-LGLPAE 401

Query: 135 P--EEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGV 192
              +  +  +S  +QQ + IAR +  + KVLILDEPT  +     + ++ +++ + ++GV
Sbjct: 402 RLLDANMLNFSGGMQQKIIIARWLLLEPKVLILDEPTKGVDIGTRQAIYGILRRIADEGV 461

Query: 193 AIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
           A++ IS   EE+  +C++V V+ DG  I       L +EK+  +   R
Sbjct: 462 AVVVISSDFEELLGVCERVVVMSDGNAIADLPSALLDEEKLTLLAAPR 509


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: 749
Number of extensions: 34
Number of successful extensions: 8
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: 634
Length adjustment: 36
Effective length of query: 458
Effective length of database: 598
Effective search space:   273884
Effective search space used:   273884
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: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources