GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Miya:8502321 DvMF_3029 ABC transporter related
           (RefSeq)
          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 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