GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimF in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate WP_068174326.1 HTA01S_RS19105 FAD-dependent oxidoreductase

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



>NCBI__GCF_001592305.1:WP_068174326.1
          Length = 684

 Score =  545 bits (1404), Expect = e-159
 Identities = 301/654 (46%), Positives = 418/654 (63%), Gaps = 16/654 (2%)

Query: 13  VAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEFGKPP 72
           +A++ +D+PP+NA SAAVR+G++  +     D  ++  VL+ AG TFIAG+D+ EFG+P 
Sbjct: 13  IAVIVIDNPPINAGSAAVRQGLMAAIETLRNDDTLEGAVLIGAGNTFIAGSDLREFGQPL 72

Query: 73  QPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVKLGLLP 132
             P L  VIAA+E   KP +AA+HG A GGG E+ALGC  RVA     +GLPEV LG++P
Sbjct: 73  TEPQLPAVIAAIEACGKPVVAALHGAAQGGGFELALGCDARVAAPGTVVGLPEVTLGIIP 132

Query: 133 GAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE-NLVAGAVAFAKKVLAE 191
           GAGGTQRLPR VG   A++MI  G  + AA AL+ GLV+ +   NL + AVA A+++  +
Sbjct: 133 GAGGTQRLPRIVGIPPAIRMICSGERVLAAAALEAGLVDLIATGNLRSAAVAHARQLKGQ 192

Query: 192 KRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGAAIDLPFEEGL 251
           KR +R    D     A+ AD +  T A     K+   ++A     DAI A   + F++GL
Sbjct: 193 KRLVR----DRQVPPASSADVATATTAAPQAGKRRPAVQAAI---DAITATAQVGFDDGL 245

Query: 252 KKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTMGGGIA 311
             ER  F +L VS ++ A R+ FFAERE+AK   + + T  RPV RVA+IGAGTMG GIA
Sbjct: 246 ADERAVFQRLRVSREAFALRHQFFAERESAKHPSLGEATA-RPVERVAVIGAGTMGSGIA 304

Query: 312 MSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGLVGLEN 371
           ++  +AG  V L+E     L+RG G +  ++ +    G L   A A   A +   +   +
Sbjct: 305 IAALDAGYRVLLLEQDAAALERGTGRIHAHYASRVQGGKLSASAAAACEARLQTSLDWAD 364

Query: 372 VKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQDVLGM 431
           +  ADL+IEAVFE + VK++VF  +DA A+PGAVLASNTSYL +D IAA T RP DV+G+
Sbjct: 365 LASADLVIEAVFEELGVKQQVFQRIDALARPGAVLASNTSYLDLDAIAAATSRPHDVIGL 424

Query: 432 HFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLAARSKQ 491
           HFFSPA+VMKL E+VRG  +APDAL T +++ K++ K+PV+ G   GF+GNR+ AA  +Q
Sbjct: 425 HFFSPAHVMKLMEVVRGQSSAPDALATGLAVGKRLKKMPVLTGNAFGFIGNRLYAAYRRQ 484

Query: 492 SEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRGIKSE-------IA 544
            E ++ EGA P+QVDA +  FG  MGPFA+ DL+GLDI WR R+ +    +       I 
Sbjct: 485 CECMVEEGAWPEQVDAALRAFGFAMGPFAVADLSGLDIAWRMRQAQAATRDPQARYVHIP 544

Query: 545 DALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDEEILERM 604
           D LCEAGR G+KTG GYY+Y +G + P  D  V  LI    A  GL+ R++ D+EI+ R 
Sbjct: 545 DRLCEAGRLGRKTGAGYYRYPEGDQGPQVDEAVHALIAQARADKGLQPRELGDDEIVRRA 604

Query: 605 VYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAE 658
           +  ++NE A +L E +A R +D+DVV + GYG+P + GGP+ +A   G   + E
Sbjct: 605 LLAIVNEAALLLAEGVAERATDVDVVLVNGYGFPRWEGGPVFWARERGAAALQE 658


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: 1115
Number of extensions: 57
Number of successful extensions: 4
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: 684
Length adjustment: 39
Effective length of query: 660
Effective length of database: 645
Effective search space:   425700
Effective search space used:   425700
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 Apr 09 2024. 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