GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimF in Dinoroseobacter shibae DFL-12

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate 3610445 Dshi_3826 3-hydroxyacyl-CoA dehydrogenase NAD-binding (RefSeq)

Query= metacyc::MONOMER-20678
         (699 letters)



>FitnessBrowser__Dino:3610445
          Length = 673

 Score =  469 bits (1208), Expect = e-136
 Identities = 288/674 (42%), Positives = 391/674 (58%), Gaps = 37/674 (5%)

Query: 9   TQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEF 68
           T   +A VTVD+PPVNA S AVR+G+L+ V         +  +L CAGRTFIAG D+ EF
Sbjct: 11  TDTGLAWVTVDNPPVNATSTAVRQGLLDAVTRV---QGARLAILRCAGRTFIAGGDMREF 67

Query: 69  GKPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVKL 128
             PPQPP L DV+ A+E S  P +A + GT LGGGLE+A+GC +R+A    + GLPEV +
Sbjct: 68  DAPPQPPDLPDVVDAIEASATPFVAVMQGTVLGGGLEIAMGCAYRIAAPGTRFGLPEVTV 127

Query: 129 GLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVENLVAGAVAFAK-- 186
           GL+PGAGGTQR PR  G + A+ M   G  + A EA   G ++ + ++  A A A     
Sbjct: 128 GLIPGAGGTQRAPRLFGWDAAIDMACAGKLLSAQEAHARGALDAIADDPEAAARALVPEP 187

Query: 187 KVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGAAIDLP 246
           ++   +RP      D +++AA +            +  +ARG  AP    DA+  A   P
Sbjct: 188 RIPVSERPAPP-PPDSARIAAHRR----------TLAARARGQTAPLQALDALLWATG-P 235

Query: 247 FEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTM 306
           F EG +KER   + L  SDQS+A R+AFFAER  A+   + D T PR ++R+A++G G M
Sbjct: 236 FREGQRKERALHLSLRASDQSRALRHAFFAERTVARPAVIRDRT-PREIARIAVMGGGLM 294

Query: 307 GGGIAMSFANAGIPVTLIE----TGEEQLKRGLGIMQKNWEATAARGGLPPDA--PAKRM 360
           G GIA +   AG  V L+E    T E    R  G++     A A R G    A   A   
Sbjct: 295 GAGIAAACLGAGYRVDLLERDAATAEAARDRVRGLI-----AGALRRGKIDQARHDAHCA 349

Query: 361 ALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAA 420
           AL TG VG+ +  +ADL IEAVFE  A K+  F A+     P A+LA+NTSYL   EI A
Sbjct: 350 ALRTG-VGIGHAAEADLAIEAVFEETATKRAAFAALAQVMAPDAILATNTSYLDPREIFA 408

Query: 421 TTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFV 480
               P   LG+HFF+PA+VMKL E+VR  +T+ + L TA ++A ++ KV V+ G+CDGF+
Sbjct: 409 GIPAPDRCLGLHFFAPAHVMKLLEVVRLPETSAETLATAFALAGRLRKVAVLSGICDGFI 468

Query: 481 GNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRGIK 540
           GNRMLAA  + +E +L +GALP+Q+D  +  +GM MGPF   DL+GL I   +R+ +   
Sbjct: 469 GNRMLAAYRRAAEYMLADGALPEQIDGAMRAYGMAMGPFEAQDLSGLHIAEANRRRQDAT 528

Query: 541 S-------EIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRR 593
                    ++D LC  GR GQ+ GKG+Y Y +G R P  DP V  LI D  A  GL RR
Sbjct: 529 RPARERYVTLSDQLCALGRTGQRAGKGWYAYAEGDRRPRVDPAVTALITDYSAAHGLPRR 588

Query: 594 DITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGL 653
                EI  R++  + NEGAR++EE IA   + +D+V L+GYG+P +RGGP+  A   G 
Sbjct: 589 THDAGEIQARLLAVLANEGARLVEEGIADSDAAVDMVKLHGYGFPRWRGGPLFAARQAGD 648

Query: 654 KHIAERLSAYAKAT 667
             I   L A   A+
Sbjct: 649 ATIRAALDALDAAS 662


Lambda     K      H
   0.317    0.134    0.383 

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: 1180
Number of extensions: 66
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 699
Length of database: 673
Length adjustment: 39
Effective length of query: 660
Effective length of database: 634
Effective search space:   418440
Effective search space used:   418440
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: 54 (25.4 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