Alignments for a candidate for xylG in Pseudovibrio axinellae Ad2

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylG in Pseudovibrio axinellae Ad2

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_068009665.1 PsAD2_RS19320 ATP-binding cassette domain-containing protein

Query= TCDB::G4FGN3
         (494 letters)



>NCBI__GCF_001623255.1:WP_068009665.1
          Length = 497

 Score =  417 bits (1073), Expect = e-121
 Identities = 223/491 (45%), Positives = 328/491 (66%), Gaps = 2/491 (0%)

Query: 1   MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE 60
           M  +LE++ I K F G++ LK V +    G V A+ GENGAGKSTLMKII+G+YQ D G 
Sbjct: 1   MTTLLELQGIEKSFSGINVLKSVDLTIRAGRVVALAGENGAGKSTLMKIISGIYQRDAGT 60

Query: 61  IIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYRE 120
           + Y+G  V + +  E+++AGI  + QEL+++ +LSVAENI++G E  +   I +  + RE
Sbjct: 61  VFYKGHEVEFTNARESMDAGIGIIHQELNLLPDLSVAENIYLGREPTKLGKIQWDVVQRE 120

Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180
           ++K++ +    +IDP   LGK SIA QQMVEIA+A+   A+V+I+DEPT +LT  ET  L
Sbjct: 121 SKKYLAQ-LKQDIDPTTPLGKLSIAQQQMVEIAKALSLNAEVIIMDEPTDALTDIETAIL 179

Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
           FEVV  L+ +G  ++FISHRL EIF++CD +++LRDG+ +   ++ +++++ ++  MVGR
Sbjct: 180 FEVVDELRAQGKGLVFISHRLGEIFQMCDDIAILRDGQMVHQGAVADISEDDLIRHMVGR 239

Query: 241 KLEKFYIKEAHEPGEVVLEVKNLSGERFENVSFSLRRGEILGFAGLVGAGRTELMETIFG 300
           +L   Y     EPG+V +EV  L+    + +SF+   GE++GFAGLVGAGRTEL + IFG
Sbjct: 240 ELSDQYPFVPAEPGDVRIEVDKLTARGAKEISFTANAGEVVGFAGLVGAGRTELAKAIFG 299

Query: 301 FRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIK 360
             P RGG + I+G+ + +  P D ++  IG V EDRK+ GL+   S+  N+SL  LDR  
Sbjct: 300 ANPIRGGSVKIDGQEISLKSPQDGVKAKIGYVTEDRKQEGLVQSQSLGSNMSLTGLDRFC 359

Query: 361 KGPFISFKREKELA-DWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILD 419
               I  K  + +     I+ F I+       +  LSGGNQQKV +AK L  +P++LILD
Sbjct: 360 NTLGIVNKTSEAVTISEYIEAFAIKTRDASTIISNLSGGNQQKVSIAKSLVPEPEVLILD 419

Query: 420 EPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAK 479
           EPTRG+DVGAK EIY ++++L  EG+ +++ISS++PE+L +SDRI V+S GKL G  D  
Sbjct: 420 EPTRGVDVGAKREIYTLINKLKAEGLCILLISSDMPELLGISDRILVLSDGKLTGSFDRD 479

Query: 480 EASQEKVMKLA 490
           EA+QE +M+ A
Sbjct: 480 EATQENIMRCA 490



 Score = 95.9 bits (237), Expect = 3e-24
 Identities = 67/236 (28%), Positives = 126/236 (53%), Gaps = 9/236 (3%)

Query: 261 KNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEIN 319
           K+ SG    ++V  ++R G ++  AG  GAG++ LM+ I G   +  G ++ +G  VE  
Sbjct: 12  KSFSGINVLKSVDLTIRAGRVVALAGENGAGKSTLMKIISGIYQRDAGTVFYKGHEVEFT 71

Query: 320 HPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLP-SLDRIKKGPFISFKREKELADWAI 378
           +  ++++ GIG++ ++   L L+  +S+  N+ L     ++ K  +   +RE +     +
Sbjct: 72  NARESMDAGIGIIHQE---LNLLPDLSVAENIYLGREPTKLGKIQWDVVQRESKKYLAQL 128

Query: 379 KTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMS 438
           K  DI P  P  K   LS   QQ V +AK L+L  +++I+DEPT  +     A ++ ++ 
Sbjct: 129 KQ-DIDPTTPLGK---LSIAQQQMVEIAKALSLNAEVIIMDEPTDALTDIETAILFEVVD 184

Query: 439 QLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494
           +L  +G G++ IS  L E+ QM D IA++  G++       + S++ +++   G E
Sbjct: 185 ELRAQGKGLVFISHRLGEIFQMCDDIAILRDGQMVHQGAVADISEDDLIRHMVGRE 240



 Score = 77.4 bits (189), Expect = 1e-18
 Identities = 59/224 (26%), Positives = 105/224 (46%), Gaps = 6/224 (2%)

Query: 21  KGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAINAG 80
           K +S     GEV    G  GAG++ L K I G      G +  +G+ +    P + + A 
Sbjct: 268 KEISFTANAGEVVGFAGLVGAGRTELAKAIFGANPIRGGSVKIDGQEISLKSPQDGVKAK 327

Query: 81  IVTVFQELS---VMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKFMK--EEFGIEI-D 134
           I  V ++     ++ + S+  N+ +   ++    +       EA    +  E F I+  D
Sbjct: 328 IGYVTEDRKQEGLVQSQSLGSNMSLTGLDRFCNTLGIVNKTSEAVTISEYIEAFAIKTRD 387

Query: 135 PEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGVAI 194
               +   S   QQ V IA+++  + +VLILDEPT  +      +++ ++  LK +G+ I
Sbjct: 388 ASTIISNLSGGNQQKVSIAKSLVPEPEVLILDEPTRGVDVGAKREIYTLINKLKAEGLCI 447

Query: 195 IFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMV 238
           + IS  + E+  I D++ VL DG+  G+   +  T+E I+   V
Sbjct: 448 LLISSDMPELLGISDRILVLSDGKLTGSFDRDEATQENIMRCAV 491


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: 635
Number of extensions: 23
Number of successful extensions: 6
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: 497
Length adjustment: 34
Effective length of query: 460
Effective length of database: 463
Effective search space:   212980
Effective search space used:   212980
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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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