GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimF in Pseudomonas fluorescens FW300-N2C3

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate AO356_30295 AO356_30295 fatty-acid oxidation protein subunit alpha

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_30295
          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:

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