GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Pseudomonas fluorescens FW300-N1B4

Align Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 (characterized)
to candidate Pf1N1B4_3903 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= SwissProt::P28793
         (715 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3903
          Length = 715

 Score = 1315 bits (3404), Expect = 0.0
 Identities = 667/715 (93%), Positives = 693/715 (96%)

Query: 1   MIYEGKAITVTALESGIVELKFDLKGESVNKFNRLTLNELRQAVDAIKADASVKGVIVSS 60
           MIYEGKAITV ALESGIVELKFDLKGESVNKFNRLTLNELRQAVD IKADAS+KGVIVSS
Sbjct: 1   MIYEGKAITVKALESGIVELKFDLKGESVNKFNRLTLNELRQAVDTIKADASIKGVIVSS 60

Query: 61  GKDVFIVGADITEFVENFKLPDAELIAGNLEANKIFSDFEDLNVPTVAAINGIALGGGLE 120
           GKDVFIVGADITEFV+NFKLPDAEL+AGNLEANKIFSDFEDLNVPTVAAINGIALGGGLE
Sbjct: 61  GKDVFIVGADITEFVDNFKLPDAELVAGNLEANKIFSDFEDLNVPTVAAINGIALGGGLE 120

Query: 121 MCLAADFRVMADSAKIGLPEVKLGIYPGFGGTVRLPRLIGVDNAVEWIASGKENRAEDAL 180
           MCLAADFRVMA++AKIGLPEVKLGIYPGFGGTVRLPR+IG DNA+EWIA+GKENRAEDAL
Sbjct: 121 MCLAADFRVMANTAKIGLPEVKLGIYPGFGGTVRLPRIIGADNAIEWIAAGKENRAEDAL 180

Query: 181 KVSAVDAVVTADKLGAAALDLIKRAISGELDYKAKRQPKLEKLKLNAIEQMMAFETAKGF 240
           KV AVDAVV  +KL  AAL+L+K AISGE DYKAKRQPKLEKLKLNAIEQMM+FETAKGF
Sbjct: 181 KVGAVDAVVAPEKLQEAALNLLKGAISGEFDYKAKRQPKLEKLKLNAIEQMMSFETAKGF 240

Query: 241 VAGQAGPNYPAPVEAIKTIQKAANFGRDKALEVEAAGFAKLAKTSASNCLIGLFLNDQEL 300
           VAGQAGPNYPAPVEAIKTIQKAANFGRDKALEVEAAGF KLAKTSA+  LIGLFLNDQEL
Sbjct: 241 VAGQAGPNYPAPVEAIKTIQKAANFGRDKALEVEAAGFVKLAKTSAAQSLIGLFLNDQEL 300

Query: 301 KKKAKVYDKIAKDVKQAAVLGAGIMGGGIAYQSASKGTPILMKDINEHGIEQGLAEAAKL 360
           KKKAK YD+IAKDVKQAAVLGAGIMGGGIAYQSASKGTPILMKDINEHGIEQGLAEAAKL
Sbjct: 301 KKKAKAYDEIAKDVKQAAVLGAGIMGGGIAYQSASKGTPILMKDINEHGIEQGLAEAAKL 360

Query: 361 LVGRVDKGRMTPAKMAEVLNGIRPTLSYGDFGNVDLVVEAVVENPKVKQAVLAEVENHVR 420
           LVGRVDKGRMTPAKMAEVLNGIRPTLSYGDFG+VDLVVEAVVENPKVKQAVLAEVE+ V+
Sbjct: 361 LVGRVDKGRMTPAKMAEVLNGIRPTLSYGDFGHVDLVVEAVVENPKVKQAVLAEVEDKVK 420

Query: 421 EDAILASNTSTISISLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSDLAVATTVA 480
           ED ILASNTSTISI+LLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSS++AVATTVA
Sbjct: 421 EDTILASNTSTISITLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSEVAVATTVA 480

Query: 481 YAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYL 540
           YAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYL
Sbjct: 481 YAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYL 540

Query: 541 MDVVGIDTGHHGRDVMAEGFPDRMKDDRRSAIDALYEAKRLGQKNGKGFYAYEADKKGKQ 600
           MDVVGIDTGHHGRDVMAEGFPDRMKDDRRSA+D LYEAKRLGQKNGKGFYAYE DK+GKQ
Sbjct: 541 MDVVGIDTGHHGRDVMAEGFPDRMKDDRRSAVDVLYEAKRLGQKNGKGFYAYETDKRGKQ 600

Query: 601 KKLVDSSVLEVLKPIVYEQRDVTDEDIINWMMIPLCLETVRCLEDGIVETAAEADMGLVY 660
           KK+ D SVLEVLKPIV+EQR+VTDEDIINWMMIPLCLETVRCLEDGIVETAAEADMGLVY
Sbjct: 601 KKVADPSVLEVLKPIVFEQREVTDEDIINWMMIPLCLETVRCLEDGIVETAAEADMGLVY 660

Query: 661 GIGFPLFRGGALRYIDSIGVAEFVALADQYAELGALYHPTAKLREMAKNGQSFFG 715
           GIGFP FRGGALRYIDSIGVAEFVALADQYA+LGALYHPTAKLR MAKNGQSFFG
Sbjct: 661 GIGFPPFRGGALRYIDSIGVAEFVALADQYADLGALYHPTAKLRAMAKNGQSFFG 715


Lambda     K      H
   0.318    0.137    0.386 

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: 1707
Number of extensions: 61
Number of successful extensions: 1
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: 715
Length of database: 715
Length adjustment: 39
Effective length of query: 676
Effective length of database: 676
Effective search space:   456976
Effective search space used:   456976
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 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