Aligments for a candidate for PS417_12065 in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Aligments for a candidate for PS417_12065 in Desulfovibrio vulgaris Hildenborough

Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein

Query= uniprot:A0A1N7TX47
         (495 letters)



>MicrobesOnline__882:206505
          Length = 524

 Score =  237 bits (605), Expect = 7e-67
 Identities = 150/472 (31%), Positives = 251/472 (53%), Gaps = 12/472 (2%)

Query: 6   LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65
           +++ E + K++  V A  D  L +  G + AL G NGAGKST +SIL G   +D G I +
Sbjct: 34  VVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHV 93

Query: 66  NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTR 125
           +G  V+F  P +AL AGI M+ Q    +  MTVAEN+ LG+    +G  +    ++R   
Sbjct: 94  DGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQ----SGAWLSPVHMSRVVA 149

Query: 126 ELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKA 185
           EL      D+D  + +  LS+ + Q VEI K    D +V+I+DEPT+ +   E + LF+A
Sbjct: 150 ELAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEA 209

Query: 186 IRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRD-HLVRGIVGQEL 244
           + R+   G  IV++SH++ E+  +AD+ +I R G  V+    +++  +  L   +VG+E+
Sbjct: 210 LHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGREV 269

Query: 245 TRIDHKVGRECA--ANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCI 302
                +V  E     +  L VD L+  G    +S ++R+GE+  I G+ G+G+ E + C+
Sbjct: 270 IL---EVAAEPLEPGDRVLHVDGLAGDG-LKGLSFEVRKGEVFAIAGVAGNGQRELVECV 325

Query: 303 YGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKR 362
            GL     G V L G P      KA    G++ + EDR+     L+  ++ N  L+A   
Sbjct: 326 TGLRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLDLVDNFLLTARGC 385

Query: 363 LSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLC 422
            +    ++ +     A D++    ++    E P  S+SGGN QK+V+ +    +P  ++ 
Sbjct: 386 FTRGPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGREFYRKPSLIVA 445

Query: 423 DEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGG 474
           + PT+G+D  A +E++  L + VR     ++VS +  E+L L+DR+AV   G
Sbjct: 446 ENPTQGLDIAATEEVWARLLE-VRSHAGVLLVSGDLNEVLALADRVAVMYRG 496



 Score = 76.6 bits (187), Expect = 2e-18
 Identities = 53/219 (24%), Positives = 106/219 (48%), Gaps = 9/219 (4%)

Query: 273 HDISLQLRQGEILGIYGLMGSGRSEFLNCIYGLTVADSGSVTLQGKPMPIGLPKATINAG 332
           HDI+L +  G I  + G  G+G+S  ++ + G    D+G + + G+ +    PK  + AG
Sbjct: 51  HDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHVDGEAVRFRSPKDALKAG 110

Query: 333 MSLVTEDRKDSGLVLTGSILSNIALSAYKRLSSWSLINARKETQLAEDMVKRLQIKTTSL 392
           + +V +      LV + ++  N+ L       S + ++    +++  ++  R  +     
Sbjct: 111 IGMVYQHFM---LVDSMTVAENVLLG-----QSGAWLSPVHMSRVVAELAARYGLDIDPA 162

Query: 393 ELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAI 452
              V  +S G +Q+V + K L  +   L+ DEPT  +  G  ++++  L +    G A +
Sbjct: 163 AR-VCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEALHRMAENGKAIV 221

Query: 453 VVSSEAPELLHLSDRIAVFKGGRLVTISTDTALSQEALL 491
            +S +  E+L L+D IA+ + G +V    ++ +  EA L
Sbjct: 222 FISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAEL 260



 Score = 50.1 bits (118), Expect = 2e-10
 Identities = 43/201 (21%), Positives = 91/201 (45%), Gaps = 10/201 (4%)

Query: 29  LRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQFNRPSEALAAGIAMITQ 88
           +R G V A+ G  G G+   +  + G+ +   G + L G P +          G+A I +
Sbjct: 302 VRKGEVFAIAGVAGNGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPE 361

Query: 89  ELEPIPY---MTVAENIWL-GREPRRAGCIVDNKALNRRTRELLDSLEFDVD---ATSPM 141
           + + +     + + +N  L  R     G  +D K+ +   R++L   E++V    A +P 
Sbjct: 362 DRQGLATCLSLDLVDNFLLTARGCFTRGPFLDRKSADAAARDIL--AEYNVQPGRAEAPA 419

Query: 142 HRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLTAQGAGIVYVSH 201
             LS   +Q + + + F     +++ + PT  +     + ++  +  + +  AG++ VS 
Sbjct: 420 RSLSGGNLQKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSH-AGVLLVSG 478

Query: 202 RLSELAQIADDYSIFRDGAFV 222
            L+E+  +AD  ++   G F+
Sbjct: 479 DLNEVLALADRVAVMYRGCFI 499


Lambda     K      H
   0.319    0.135    0.381 

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: 592
Number of extensions: 33
Number of successful extensions: 8
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: 495
Length of database: 524
Length adjustment: 34
Effective length of query: 461
Effective length of database: 490
Effective search space:   225890
Effective search space used:   225890
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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