Aligments for a candidate for pimF in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Aligments for a candidate for pimF in Pseudomonas fluorescens FW300-N2E2

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate Pf6N2E2_1922 Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1922
          Length = 703

 Score =  550 bits (1416), Expect = e-160
 Identities = 319/704 (45%), Positives = 439/704 (62%), Gaps = 22/704 (3%)

Query: 2   SEVVTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIA 61
           S +V+   +  VA++TV++PPVNAL+  +R  I++ V  A ADPAV AIVL+  G+ FIA
Sbjct: 4   SLMVSYEVEGVVAVITVNNPPVNALTPEMRGSIIDAVTHANADPAVAAIVLMGGGQNFIA 63

Query: 62  GADITEFGKPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKL 121
           GADI +FGK  +    +   AAL+ S KPT+AAIHG ALGGGLE AL CH+R+A+  AKL
Sbjct: 64  GADIRQFGKA-RTITTSMSAAALDASAKPTVAAIHGYALGGGLEHALACHYRIALPTAKL 122

Query: 122 GLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVV-----EN 176
           GLPEV LGL+PG GGTQRLPR VG  +A  ++V    I A EAL+ GL+ ++V     + 
Sbjct: 123 GLPEVALGLIPGGGGTQRLPRLVGAAVATDLLVSSRHIHAPEALQIGLISQIVPGTQNQE 182

Query: 177 LVAGAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAM---TKKARGLEAPF 233
           L   AV +AK V A  +P +R+RD    LA    D +      AA     KK+   +AP 
Sbjct: 183 LRDAAVRYAKAV-AHAQP-QRVRD----LALEPMDATTMDLLQAARREAAKKSPHNKAPQ 236

Query: 234 ACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPR 293
              D I AA +LPF+E L+ E   F +L  SD +KA RYAFFAEREAAKV   P G KP 
Sbjct: 237 YAIDCIEAAFNLPFDEALEVESRLFSELEGSDVAKALRYAFFAEREAAKVPDAPPGFKPA 296

Query: 294 PVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPP 353
            V+  A+IGAGTMG GIA+ FA+AGI V L+E   E L RGL  ++  +     RG +  
Sbjct: 297 GVTSAAVIGAGTMGAGIAICFADAGIVVKLLEASAEALDRGLQRIRDIYAVKVKRGRMTV 356

Query: 354 DAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYL 413
                 +  +  +   E + D D+++EAVFE + +KK+VFT +DA  KPGA+L +N+S +
Sbjct: 357 QEMDACLQFVQPVSHYEEIGDCDVVVEAVFERIDLKKDVFTKLDAVMKPGALLLTNSSAI 416

Query: 414 SIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVV 473
            I+ +A  T RPQ V G HFF+PAN MKLCEIV+G +T+ + ++ A+ + + + KV  V 
Sbjct: 417 DINVMANMTGRPQSVAGAHFFAPANAMKLCEIVKGDQTSIETVVRAMKMGRDLKKVCAVS 476

Query: 474 GVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRS 533
           G CDGF  NR  A    +   LL EGA P+Q+D V+ +FG PMGPFA+ DL+GLD+ + +
Sbjct: 477 GTCDGFAANRSRAPLVTEMMLLLEEGARPEQIDRVMVEFGYPMGPFAVSDLSGLDVSYDT 536

Query: 534 RKDRGI------KSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAK 587
           RK R        K  + D + E GR GQK G G+Y+YE+G R P  D EV  +I     +
Sbjct: 537 RKRRAAADPQYRKLHVPDRMVELGRKGQKNGAGWYRYEEGDRTPRHDEEVMRIIATVAHE 596

Query: 588 LGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHY 647
           LG  +R  TD EIL+R+++  INE  +IL+E  A R SDIDV+WLYG+G+P +RGG +++
Sbjct: 597 LGTPQRTFTDSEILKRLLFASINEACKILDEGKAYRASDIDVMWLYGFGFPRHRGGLLYW 656

Query: 648 ADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTFASL 691
           AD++G   I  ++  + +        P+PLL++ A EG +   L
Sbjct: 657 ADTIGATEIHLQVQQWHEQYG-RRWAPSPLLSKAANEGLSLREL 699


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: 1088
Number of extensions: 46
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: 703
Length adjustment: 39
Effective length of query: 660
Effective length of database: 664
Effective search space:   438240
Effective search space used:   438240
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 paper from 2022 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