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

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__Dino:3610445 Dshi_3826 3-hydroxyacyl-CoA
           dehydrogenase NAD-binding (RefSeq)
          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:

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 preprint 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