GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11890 in Desulfovibrio vulgaris Miyazaki F

Align Inositol transport system ATP-binding protein (characterized)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)

Query= reanno::WCS417:GFF2332
         (517 letters)



>FitnessBrowser__Miya:8502321
          Length = 537

 Score =  271 bits (694), Expect = 3e-77
 Identities = 168/494 (34%), Positives = 274/494 (55%), Gaps = 14/494 (2%)

Query: 21  PYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEI 80
           P ++ +  I K F  V A  D+ L +RPG + AL+GENGAGKSTLM I+AG  + DAG I
Sbjct: 27  PPVVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTI 86

Query: 81  RLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRC 140
            + G P VF +P  A +AGI M++Q   L+  M++AEN+ +G+     L     R+    
Sbjct: 87  VVDGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLGQSPDMLLRPARMRDE--- 143

Query: 141 TAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLF 200
            A L  R  + +DP  +VG LS+ ERQ VEI K +  DS +LI+DEPT+ +T +E   LF
Sbjct: 144 VAALAERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLF 203

Query: 201 SIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIG-LQRADSMNSDSLISMMVGR 259
             +  +  QGK +V+I+HK+ EV  +ADE+A+ R G  +     AD  N   L + MVGR
Sbjct: 204 EAMWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGR 263

Query: 260 E-LSQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETI 318
           + + Q+   R TP+ D +L+V  L+  G+  DVS  +  GEI+ IAG+ G+G+  + E I
Sbjct: 264 DVVLQVDAKRLTPV-DTVLSVEHLSGAGL-SDVSLQVRRGEIVAIAGVAGNGQKELVEAI 321

Query: 319 FGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPC--LSVLENMEMAVL 376
            G+    +G++ + G+  R         +G A + EDR+  GL  C  L +++N  +   
Sbjct: 322 CGLARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQ--GLATCRHLDLVDNFLLTTR 379

Query: 377 PHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLL 436
             +    F+ +       + +  +  V+   +      LSGGN QK ++ R     P ++
Sbjct: 380 NQFAKGVFLDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFRKPEVI 439

Query: 437 ILDEPTRGIDVGAKAEIY-RLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGT 495
           + + PT+G+D+ A  E++ RL+   ++ G  V++++ +L E L ++DR+ VM+ G  +  
Sbjct: 440 VAENPTQGLDISATEEVWGRLLEARSTSG--VLLVTGDLNEALELADRIAVMYRGRFIDV 497

Query: 496 LDRSEATQEKVMQL 509
            D+ +  + + + L
Sbjct: 498 FDKDDTAKVQAIGL 511



 Score = 68.6 bits (166), Expect = 6e-16
 Identities = 52/224 (23%), Positives = 100/224 (44%), Gaps = 6/224 (2%)

Query: 39  LADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFETPLAAQKA 98
           L+DV L+VR G ++A+ G  G G+  L++ I G+ +P+AGE+R+ G+P          + 
Sbjct: 291 LSDVSLQVRRGEIVAIAGVAGNGQKELVEAICGLARPEAGEVRILGRPWREFFAGPPGRR 350

Query: 99  GIAMI---HQELNLMPHMSIAENIWIG-REQLNSLHMVNHREMHRCTAELLARLRINL-D 153
           G+A I    Q L    H+ + +N  +  R Q      ++  E       ++    +   D
Sbjct: 351 GLAYIPEDRQGLATCRHLDLVDNFLLTTRNQFAKGVFLDRTEATNAVKRVVWEYNVQPGD 410

Query: 154 PEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIADLKSQGKGI 213
                  LS    Q + I +      ++++ + PT  +       ++  + + +S   G+
Sbjct: 411 ITAPARALSGGNLQKLVIGREFFRKPEVIVAENPTQGLDISATEEVWGRLLEARSTS-GV 469

Query: 214 VYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMV 257
           + +T  +NE   +AD +AV   G +I +   D       I +M+
Sbjct: 470 LLVTGDLNEALELADRIAVMYRGRFIDVFDKDDTAKVQAIGLMM 513


Lambda     K      H
   0.320    0.136    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: 580
Number of extensions: 30
Number of successful extensions: 9
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: 517
Length of database: 537
Length adjustment: 35
Effective length of query: 482
Effective length of database: 502
Effective search space:   241964
Effective search space used:   241964
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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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:

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:

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:

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:

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