Aligments for a candidate for mglA in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Aligments for a candidate for mglA in Shewanella sp. ANA-3

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 7024900 Shewana3_2074 ABC transporter related (RefSeq)

Query= TCDB::G4FGN3
         (494 letters)



>lcl|FitnessBrowser__ANA3:7024900 Shewana3_2074 ABC transporter
           related (RefSeq)
          Length = 499

 Score =  387 bits (993), Expect = e-112
 Identities = 204/499 (40%), Positives = 324/499 (64%), Gaps = 10/499 (2%)

Query: 1   MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE 60
           M  ILE+K I K +PGV AL+ VS+  + GEVHA++GENGAGKSTL+K++ G    D G+
Sbjct: 1   MSLILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGD 60

Query: 61  IIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYRE 120
           I++ G    +N P +A  AGI TV+QE++++ NL+VA+N+F+G E +R   I +KKMY +
Sbjct: 61  ILFLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYAD 120

Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180
           A   + + F ++ID    L  YSIA+QQ++ IAR V   AKVL+LDEPT+SL  KE + L
Sbjct: 121 ARAVLTQ-FKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVL 179

Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
           F ++  LK KGVAI+FI+H L+++++I D+++VLR+G++IG      L + K++E M+GR
Sbjct: 180 FGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGR 239

Query: 241 KLEKFYIKEAHEPGEVV--------LEVKNLSGERFENVSFSLRRGEILGFAGLVGAGRT 292
            L++  + +  +   V         LE  ++ G   ++++ ++ +G+ +G AGL+G+GR+
Sbjct: 240 SLQEQLVDKQEKERTVTRAEAVLLSLEDVSVKGS-IQSMNLTVPKGQAVGLAGLLGSGRS 298

Query: 293 ELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVS 352
           E+   +FG      G I++ G+++ ++ P+DAI  GI L PEDRK  G+I  +SI  N+ 
Sbjct: 299 EVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENII 358

Query: 353 LPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALK 412
           L    RI    ++S  R++E+A + I    I     D+ +  LSGGNQQKV+LA+WLA++
Sbjct: 359 LALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIE 418

Query: 413 PKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKL 472
           P +L+LDEPTRGID+GA AEI +++  L  EG+ +++ SSEL E++  S+++ V+     
Sbjct: 419 PILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYA 478

Query: 473 AGIIDAKEASQEKVMKLAA 491
              +   E + + VM+  A
Sbjct: 479 VRELSGAELTSQHVMQAIA 497



 Score = 92.8 bits (229), Expect = 2e-23
 Identities = 70/246 (28%), Positives = 123/246 (50%), Gaps = 19/246 (7%)

Query: 256 VVLEVKNLSG-----ERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIY 310
           ++LE+K +S      +  E+VS  L  GE+    G  GAG++ L++ + G + K  G+I 
Sbjct: 3   LILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDIL 62

Query: 311 IEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKRE 370
             G+    N P+DA + GI  V ++   + L+  +++  N+ L    R  +   I FK+ 
Sbjct: 63  FLGEPQHFNTPMDAQKAGISTVYQE---VNLVPNLTVAQNLFLGYEPR--RLGLIHFKKM 117

Query: 371 KELADWAIKTF----DIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGID 426
              A   +  F    D+     D  +       QQ + +A+ +A+  K+L+LDEPT  +D
Sbjct: 118 YADARAVLTQFKLDIDVSAPLSDYSIAV-----QQLIAIARGVAMSAKVLVLDEPTASLD 172

Query: 427 VGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKV 486
                 ++ I++QL  +GV ++ I+  L +V Q+SDRI V+  G+  G     E  Q K+
Sbjct: 173 AKEVQVLFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKL 232

Query: 487 MKLAAG 492
           ++   G
Sbjct: 233 IEAMLG 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: 596
Number of extensions: 28
Number of successful extensions: 7
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: 499
Length adjustment: 34
Effective length of query: 460
Effective length of database: 465
Effective search space:   213900
Effective search space used:   213900
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