Alignments for a candidate for mglA in Rhodobacter ovatus JA234

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Rhodobacter ovatus JA234

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_097031110.1 CRO07_RS12930 ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>NCBI__GCF_900207575.1:WP_097031110.1
          Length = 506

 Score =  286 bits (731), Expect = 2e-81
 Identities = 162/480 (33%), Positives = 273/480 (56%), Gaps = 13/480 (2%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           P+L +  I KRF  + A   +S+    GEV A++GENGAGK+TLM I+ G Y  D G + 
Sbjct: 5   PVLRLCGITKRFGSLVANDAISLSLNRGEVVALLGENGAGKTTLMNILFGHYVADAGTVE 64

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEE--KRGIFIDYKKMYRE 120
             G+ +   HP  A+ AG+  V Q  ++ DNL+V +NI +G     + G+    K + R 
Sbjct: 65  VMGQPLPPGHPRAALAAGVGMVHQHFTLADNLTVLDNILLGTRPLWRPGL---RKAVARA 121

Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180
             + + ++FG+ + P+ ++G  S+  +Q VEI +A+Y+ A++LILDEPT+ LT +ETE L
Sbjct: 122 RVQALSQDFGLSVHPDARVGTLSVGERQRVEILKALYRDARILILDEPTAVLTPQETEAL 181

Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
           F  ++    +G++IIFISH+L E+  + D+  VLR G  +G  +  +  +  +  +MVG 
Sbjct: 182 FRTLRLAVGRGLSIIFISHKLHEVMGVADRAVVLRHGRVVGEVATADTDRHALAALMVGE 241

Query: 241 KLEKFYIKEAHEPGEVVLEVKNLSGER------FENVSFSLRRGEILGFAGLVGAGRTEL 294
           ++    +     PG V+L + +++  +         V+  LR G I G AG+ G G+  L
Sbjct: 242 EVVPPKVAPP-TPGPVLLRLDDVTTAQAGTATGLRRVTLDLRAGTITGLAGVSGNGQAAL 300

Query: 295 METIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLP 354
            + + G    + G ++I G  V    P +A+  GI  +PEDR   G I   ++  N  L 
Sbjct: 301 SDLVSGVIRPQAGRLHIAGAPVTHWTPREAVGAGIARIPEDRHSTGTIADFTLTENAILE 360

Query: 355 SL-DRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKP 413
               R  KG +++++  +  A+  I+T+D+R   PD ++  LSGGN QK++L + L   P
Sbjct: 361 GYRSRFAKGGWMNWRAARAFAEGIIRTYDVRCPGPDTRIRLLSGGNMQKLILGRVLEPGP 420

Query: 414 KILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLA 473
           +I++ ++P RG+D+GA   ++  + Q    G  V++IS +L E++ +SD I V+S G+L+
Sbjct: 421 RIILANQPVRGLDIGAITYVHSRLLQARDAGAAVLLISEDLDEIMALSDSIHVISEGRLS 480



 Score = 92.8 bits (229), Expect = 2e-23
 Identities = 64/224 (28%), Positives = 111/224 (49%), Gaps = 6/224 (2%)

Query: 271 VSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIG 330
           +S SL RGE++   G  GAG+T LM  +FG      G + + G+ +   HP  A+  G+G
Sbjct: 25  ISLSLNRGEVVALLGENGAGKTTLMNILFGHYVADAGTVEVMGQPLPPGHPRAALAAGVG 84

Query: 331 LVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDR 390
           +V    +   L   ++++ N+ L +    + G   +  R +  A    + F +   +PD 
Sbjct: 85  MV---HQHFTLADNLTVLDNILLGTRPLWRPGLRKAVARARVQA--LSQDFGLS-VHPDA 138

Query: 391 KVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMI 450
           +V  LS G +Q+V + K L    +ILILDEPT  +       ++R +      G+ +I I
Sbjct: 139 RVGTLSVGERQRVEILKALYRDARILILDEPTAVLTPQETEALFRTLRLAVGRGLSIIFI 198

Query: 451 SSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494
           S +L EV+ ++DR  V+  G++ G +   +  +  +  L  G E
Sbjct: 199 SHKLHEVMGVADRAVVLRHGRVVGEVATADTDRHALAALMVGEE 242



 Score = 60.8 bits (146), Expect = 1e-13
 Identities = 44/226 (19%), Positives = 103/226 (45%), Gaps = 6/226 (2%)

Query: 20  LKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAINA 79
           L+ V+++   G +  + G +G G++ L  +++GV +P  G +   G  V    P EA+ A
Sbjct: 274 LRRVTLDLRAGTITGLAGVSGNGQAALSDLVSGVIRPQAGRLHIAGAPVTHWTPREAVGA 333

Query: 80  GIVTVFQE---LSVMDNLSVAENIFMGDEEKR---GIFIDYKKMYREAEKFMKEEFGIEI 133
           GI  + ++      + + ++ EN  +     R   G +++++     AE  ++       
Sbjct: 334 GIARIPEDRHSTGTIADFTLTENAILEGYRSRFAKGGWMNWRAARAFAEGIIRTYDVRCP 393

Query: 134 DPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGVA 193
            P+ ++   S    Q + + R +    ++++ ++P   L       +   +   ++ G A
Sbjct: 394 GPDTRIRLLSGGNMQKLILGRVLEPGPRIILANQPVRGLDIGAITYVHSRLLQARDAGAA 453

Query: 194 IIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVG 239
           ++ IS  L+EI  + D + V+ +G      +   +T++++   M G
Sbjct: 454 VLLISEDLDEIMALSDSIHVISEGRLSPGFARGTMTQQQLGLWMAG 499


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: 554
Number of extensions: 30
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 494
Length of database: 506
Length adjustment: 34
Effective length of query: 460
Effective length of database: 472
Effective search space:   217120
Effective search space used:   217120
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 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 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