Alignments for a candidate for mglA in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Caulobacter crescentus NA1000

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 CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__Caulo:CCNA_00903
          Length = 515

 Score =  374 bits (961), Expect = e-108
 Identities = 201/498 (40%), Positives = 319/498 (64%), Gaps = 11/498 (2%)

Query: 4   ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63
           +L+V  + K FPGV AL  V +    GEVHA++GENGAGKSTL+KI++  +  D G + +
Sbjct: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62

Query: 64  EGRGVR-WNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAE 122
            G+ +   + P      GI T++QE ++   LSVAEN+++G E +R   +D+ ++  +A+
Sbjct: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQ 122

Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182
             + +  G+ ++P+  +   ++A QQMVEIA+A+   A+++I+DEPT++L+ +E ++L  
Sbjct: 123 ALLND-LGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181

Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242
           ++  LK + V++I++SHRL E+  +CD+ +V+RDG ++ +  + ++    +V +MVGR +
Sbjct: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241

Query: 243 EKFYIKEAHEPGEVVLEVKNLSGER--------FENVSFSLRRGEILGFAGLVGAGRTEL 294
           E    K    PG VVL+V+ ++              VSF+ R GEI+G AGLVGAGRT+L
Sbjct: 242 EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301

Query: 295 METIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLP 354
              IFG  P   G + ++ K + +  P DAI+ GI LVPEDRK+ G  L  SI  N+SLP
Sbjct: 302 ARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP 361

Query: 355 SLDRIKK-GPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKP 413
           SL  +   G ++  + E++L +   +   I+ A  +  +  LSGGNQQKV+L + +AL P
Sbjct: 362 SLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTP 421

Query: 414 KILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLA 473
           K+LI+DEPTRGID+GAKAE+++++S LA  GV V++ISSEL EV+ +SDRI V   G + 
Sbjct: 422 KVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIV 481

Query: 474 GIIDAKEASQEKVMKLAA 491
             +DA+ A++E +M   A
Sbjct: 482 ADLDAQTATEEGLMAYMA 499



 Score = 66.2 bits (160), Expect = 3e-15
 Identities = 62/241 (25%), Positives = 100/241 (41%), Gaps = 22/241 (9%)

Query: 261 KNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEIN 319
           K+  G R  + V   +  GE+    G  GAG++ L++ +        G +   G+ ++  
Sbjct: 11  KSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD-- 68

Query: 320 HPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIK 379
            P DA        P  R++LG+  I    +    P L   +        R   L DW+  
Sbjct: 69  -PRDA--------PLRRQQLGIATIYQEFN--LFPELSVAENMYLGREPRRLGLVDWSRL 117

Query: 380 TFDIR--------PAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKA 431
             D +        P  PD  V  L+   QQ V +AK + L  +++I+DEPT  +      
Sbjct: 118 RADAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVD 177

Query: 432 EIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAA 491
            ++ I++ L    V VI +S  L EV  M DR  VM  G+     D  +     +++L  
Sbjct: 178 RLHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMV 237

Query: 492 G 492
           G
Sbjct: 238 G 238


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: 640
Number of extensions: 28
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: 515
Length adjustment: 34
Effective length of query: 460
Effective length of database: 481
Effective search space:   221260
Effective search space used:   221260
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:

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, 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

GapMind for catabolism of small carbon sources