Alignments for a candidate for pimF in Sphingobium czechense LL01

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_066600973.1 V473_RS04345 3-hydroxyacyl-CoA dehydrogenase

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



>NCBI__GCF_001046645.1:WP_066600973.1
          Length = 723

 Score =  305 bits (781), Expect = 5e-87
 Identities = 221/731 (30%), Positives = 343/731 (46%), Gaps = 60/731 (8%)

Query: 1   MSEVVTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIV---LVCAGR 57
           M+ +      D +A +T+D P  +     +    L +++AA+   A +  +   ++ +G+
Sbjct: 1   MNTIAFDIDADGIATLTIDVPGQSM--NVIGPDFLADLDAAITRIASEEGIKGAVIASGK 58

Query: 58  T--FIAGADITEFGK-------PPQPPALND-------VIAALENSPKPTIAAIHGTALG 101
              F+AG D+  FG         P P AL D       +   LE S KP   AI G  +G
Sbjct: 59  DSGFMAGMDLKFFGAMLAKAGDAPAPAALYDDLFVLNALFRRLETSGKPVACAIEGACVG 118

Query: 102 GGLEVALGCHFRVAVKEAK--LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPI 159
           GG E+AL CH R      K  LGLPE+ +GL PG GG+QRLPR +G + A+  ++ G   
Sbjct: 119 GGFELALACHRRFVGDSPKTQLGLPEILIGLFPGGGGSQRLPRIMGVQAALMYMLQGKLF 178

Query: 160 GAAEALKHGLVEEVVENLVAGAVAFAKKVLAEKRPLRRLRDDDSK----LAAAKADRSIF 215
             AEA    +V+ VV     G    A +   +  P    +  D K       A      F
Sbjct: 179 RPAEAAMLKVVDAVVPQ---GTAVTAAREWVKANPNATSQPWDVKGYKVPGGAGGFNPGF 235

Query: 216 TNAVAA---MTKKA--RGLEAPFACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQ 270
              +A    MT K   R + AP A   A+   I LP +  ++ E + F K+    Q+   
Sbjct: 236 VQTMAGALPMTLKQTQRNMHAPIALLSAVYEGITLPMDRAIRIESQYFAKVAADPQASNM 295

Query: 271 RYAFFAEREAAKVDGV-PDGTKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEE 329
               F  ++AA+     P G    P  ++A++GAG MG GIA   A AGI V L +    
Sbjct: 296 IRTLFVNKQAAERGARRPKGEAKAPTQKLAMLGAGMMGAGIATVAAQAGIEVVLFDRDLA 355

Query: 330 QLKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVK 389
             ++G   ++   +    +G + P+   + +A +T      ++  AD +IEAVFE +++K
Sbjct: 356 YAQKGKAHVEDVLKKRLGKG-MTPEKLEQTLARVTPTTDYADLAGADFVIEAVFEDVSIK 414

Query: 390 KEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGA 449
            EV   V+       +  SNTS L I ++A    +P++ +G+HFFSP   M L EI+ G 
Sbjct: 415 AEVTKKVEEVLGADTIFGSNTSTLPITKLAQAWTKPENFIGVHFFSPVEKMPLVEIILGE 474

Query: 450 KTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVV 509
           KT P A+  A+    +I K P+VV    GF  +R      ++  +L+ EG  P  ++   
Sbjct: 475 KTGPAAIAKALDFVSQIKKTPIVVHDSRGFYTSRSFGTYVQEGAELVGEGVNPALIENAG 534

Query: 510 TKFGMPMGPFAMGDLAGLDIGWRSRKDRGIKSEIADA------------LCEAGRFGQKT 557
            + GMP GP A+ D   +++GW+       K E+ DA            + EAGR G+K 
Sbjct: 535 KQLGMPTGPLAVSDEVSIELGWKIMS--AAKKELGDAYVPQGSDDIMVQMVEAGRLGRKN 592

Query: 558 GKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDEEILERMVYPMINEGARILE 617
           GKG+Y Y  G +  +  P +  +      + G+       E + ER++Y  + E AR   
Sbjct: 593 GKGWYDYPAGGKKYL-SPVLGEMFPRAAEQPGV-------EAVKERLLYRQLIECARCFA 644

Query: 618 EKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAERLSAYAKATNDPSLEPAPL 677
           E +   P D D+  ++G+G+  Y GGP  + D+VG+ H+   L   A A + P   P   
Sbjct: 645 EGVLETPEDGDIGAIFGWGFAPYTGGPFSHMDTVGIAHVVAVLDRLA-AAHGPRFAPTAQ 703

Query: 678 LARLAAEGKTF 688
           L  +AA G TF
Sbjct: 704 LREMAASGATF 714


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: 1080
Number of extensions: 55
Number of successful extensions: 7
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: 723
Length adjustment: 39
Effective length of query: 660
Effective length of database: 684
Effective search space:   451440
Effective search space used:   451440
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: 55 (25.8 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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