GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimF in Sphingobium czechense LL01

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate WP_066599254.1 V473_RS00615 hypothetical protein

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



>NCBI__GCF_001046645.1:WP_066599254.1
          Length = 689

 Score =  506 bits (1302), Expect = e-147
 Identities = 297/693 (42%), Positives = 412/693 (59%), Gaps = 26/693 (3%)

Query: 13  VAIVTVDSPPVNALSAA--VRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEF-G 69
           V +V  D+ PVNAL+    + + I   V  A  D  V AI+L   G  F AGADI +F G
Sbjct: 11  VLVVRFDNSPVNALTVGGGLVQAIERRVAQAQTDERVDAIILTGGGTVFSAGADIADFEG 70

Query: 70  KPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVKLG 129
            P +  A+  ++ ++EN  KP +AAI G  LGGGLE+AL  HFRVA   AK G PE+ LG
Sbjct: 71  APERIDAIRSLMQSIENCRKPVVAAIEGLCLGGGLELALAAHFRVASSTAKFGFPEISLG 130

Query: 130 LLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE-NLVAGAVAF--AK 186
           LLPG GGTQR PR  G   A+ +++ G  + AA+AL+ GL++ + E ++V  A+A   A 
Sbjct: 131 LLPGGGGTQRSPRLAGAGNAIDLMLSGKSVSAAKALEIGLIDRIAEGDVVEAALAMLAAG 190

Query: 187 KVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGAAIDLP 246
            V + +R        D   A   A+R         +T   R +    AC  AI A  DL 
Sbjct: 191 LVGSTRRSGSLPVPQDLDAAIDSAERR------TGLTDAGRAI---IACVRAI-AQTDL- 239

Query: 247 FEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTM 306
            + GLK E E F  L+ S+QS+A R+AFF  R   K+ G     + + V  V ++G G M
Sbjct: 240 -QAGLKLEAEQFGALMTSEQSRALRHAFFGRRIVGKIPGGVR-VESKGVRHVTVVGGGLM 297

Query: 307 GGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGL 366
           G GIA+S  NA + VT++E   E   +    ++ +    A +  +      +R+  +   
Sbjct: 298 GTGIAISLLNADLGVTVVEAKPEGFDKCRASIEASLRRDADKARITAATADRRIGALNMG 357

Query: 367 VGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQ 426
             ++    +DL IEAVFE M  K+EVF A+D  A  GA+LASNTS L +D IA  T RP+
Sbjct: 358 RSIDEAMPSDLYIEAVFEDMDAKREVFQALDRIAPLGAILASNTSTLDLDAIAQFTSRPE 417

Query: 427 DVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLA 486
            V+G+HFFSPAN+M+L E+VRGA+T+P+ L +A++ AK I K  VV GVCDGF+GNR+  
Sbjct: 418 AVVGLHFFSPANIMRLLEVVRGARTSPETLASAMAFAKSIGKTGVVAGVCDGFIGNRIFE 477

Query: 487 ARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRGIK------ 540
              +Q+  LL EGALP Q+DA +  FGM MGP  + DLAG DIGW  RK R ++      
Sbjct: 478 EYLRQAWFLLEEGALPHQIDAALEAFGMAMGPCRVMDLAGQDIGWNIRKRRAVEQPDRPY 537

Query: 541 SEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDEEI 600
           S+I D +CE GRFGQKTG G+Y Y  G R P  DP +E LI     ++   RR I D EI
Sbjct: 538 SKIPDLVCELGRFGQKTGTGFYLYPDG-RTPQRDPLIEALIVSHSRQIDFDRRVIDDSEI 596

Query: 601 LERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAERL 660
           +ER ++ MINEGA+++ E IA RP D+D+++L GYG+P  RGGPM +AD VGL H+ E++
Sbjct: 597 VERCIFAMINEGAKLVGEGIAYRPVDVDIIYLDGYGFPASRGGPMFHADQVGLPHLLEKM 656

Query: 661 SAYAKATNDPSLEPAPLLARLAAEGKTFASLTQ 693
           + YA+  +  + EPAPL+  L+ + + F  L +
Sbjct: 657 AQYARGHHGWAWEPAPLILELSDKNQKFGDLNR 689


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: 1086
Number of extensions: 50
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: 689
Length adjustment: 39
Effective length of query: 660
Effective length of database: 650
Effective search space:   429000
Effective search space used:   429000
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 24 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