Aligments for a candidate for fadB in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for fadB in Pseudomonas simiae WCS417

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 GFF1489 PS417_07575 multifunctional fatty acid oxidation complex subunit alpha

Query= SwissProt::P28793
         (715 letters)



>FitnessBrowser__WCS417:GFF1489
          Length = 715

 Score = 1308 bits (3385), Expect = 0.0
 Identities = 667/715 (93%), Positives = 689/715 (96%)

Query: 1   MIYEGKAITVTALESGIVELKFDLKGESVNKFNRLTLNELRQAVDAIKADASVKGVIVSS 60
           MIYEGKAITV ALESGIVELKFDLKGESVNKFNRLTLNELRQAVD IKADASVKGVIVSS
Sbjct: 1   MIYEGKAITVKALESGIVELKFDLKGESVNKFNRLTLNELRQAVDTIKADASVKGVIVSS 60

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

Query: 121 MCLAADFRVMADSAKIGLPEVKLGIYPGFGGTVRLPRLIGVDNAVEWIASGKENRAEDAL 180
           MCLAADFRVM+ +AKIGLPEVKLGIYPGFGGTVRLPRLIG DNA+EWIA+GKEN+AEDAL
Sbjct: 121 MCLAADFRVMSATAKIGLPEVKLGIYPGFGGTVRLPRLIGADNAIEWIAAGKENKAEDAL 180

Query: 181 KVSAVDAVVTADKLGAAALDLIKRAISGELDYKAKRQPKLEKLKLNAIEQMMAFETAKGF 240
           KV AVDAVV  DKL  AAL+LIK AISGE DYKAKRQPKLEKLKLNAIEQMM+FETAKGF
Sbjct: 181 KVGAVDAVVAPDKLAEAALNLIKGAISGEFDYKAKRQPKLEKLKLNAIEQMMSFETAKGF 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
           LVGRVDKGRMT AKMAEVLNGIRPTLSYGDFG+VDLVVEAVVENPKVKQAVLAEVE  V+
Sbjct: 361 LVGRVDKGRMTAAKMAEVLNGIRPTLSYGDFGHVDLVVEAVVENPKVKQAVLAEVEAQVK 420

Query: 421 EDAILASNTSTISISLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSDLAVATTVA 480
           +D ILASNTSTISISLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSS+LAVATTVA
Sbjct: 421 DDTILASNTSTISISLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSELAVATTVA 480

Query: 481 YAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYL 540
           YAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYL
Sbjct: 481 YAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYL 540

Query: 541 MDVVGIDTGHHGRDVMAEGFPDRMKDDRRSAIDALYEAKRLGQKNGKGFYAYEADKKGKQ 600
           MDVVGIDTGHHGRDVMAEGFPDRMKDDRRSAIDALYEAKRLGQKNGKGFYAYEADKKGKQ
Sbjct: 541 MDVVGIDTGHHGRDVMAEGFPDRMKDDRRSAIDALYEAKRLGQKNGKGFYAYEADKKGKQ 600

Query: 601 KKLVDSSVLEVLKPIVYEQRDVTDEDIINWMMIPLCLETVRCLEDGIVETAAEADMGLVY 660
           KK+ D SV EVL P++YEQR+V+DEDIINWMMI LCLETVRCLEDGIVETAAEADMGLVY
Sbjct: 601 KKVADPSVHEVLAPVIYEQREVSDEDIINWMMIALCLETVRCLEDGIVETAAEADMGLVY 660

Query: 661 GIGFPLFRGGALRYIDSIGVAEFVALADQYAELGALYHPTAKLREMAKNGQSFFG 715
           GIGFP FRGGALRYIDSIGVAEFVALAD+YA+LG LYHPTAKLREMAKNGQSFFG
Sbjct: 661 GIGFPPFRGGALRYIDSIGVAEFVALADKYADLGPLYHPTAKLREMAKNGQSFFG 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: 1704
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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Candidates (tab-delimited)
Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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