Alignments for a candidate for fadB in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Pseudomonas stutzeri RCH2

Align fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized)
to candidate GFF2604 Psest_2654 fatty oxidation complex, alpha subunit FadB

Query= metacyc::MONOMER-17591
         (715 letters)



>FitnessBrowser__psRCH2:GFF2604
          Length = 715

 Score = 1261 bits (3262), Expect = 0.0
 Identities = 633/715 (88%), Positives = 679/715 (94%)

Query: 1   MIYQGKAITVKPLEGGIVELNFDLKGESVNKFNRLTLSELRAAVDAIKADASVKGVIVTS 60
           MIY+GKAITVK LE GIVELNFDLKGESVNKFNRLTL++LR AVDAIKADASVKGVIVTS
Sbjct: 1   MIYEGKAITVKALESGIVELNFDLKGESVNKFNRLTLNDLRQAVDAIKADASVKGVIVTS 60

Query: 61  GKDVFIVGADITEFVDNFQLPDEELMAGNLEANKIFSDFEDLDVPTVAAINGIALGGGLE 120
           GKDVFIVGADITEFVDNF++ DEEL+AGNLEANKIFSDFEDL VPTVAAINGIALGGG E
Sbjct: 61  GKDVFIVGADITEFVDNFKMADEELVAGNLEANKIFSDFEDLGVPTVAAINGIALGGGFE 120

Query: 121 MCLAADFRVMSATAKVGLPEVKLGIYPGFGGTVRLPRLIGCDNAVEWIASGKENKAEDAL 180
           MC+AAD+RVMS TAKVGLPEVKLGIYPGFGGTVRLPRLIG DNAVEWIASGKEN+AEDAL
Sbjct: 121 MCMAADYRVMSTTAKVGLPEVKLGIYPGFGGTVRLPRLIGVDNAVEWIASGKENRAEDAL 180

Query: 181 KVGAVDAVVAPEQLQAAALDLAKRAVAGELDHKARRQPKLEKLKLNAIEQMMAFETAKGF 240
           KV AVDAVVAP++LQAAALDL KRA++GELD+KA+RQPKL+KLKLNAIEQMMAFET+K F
Sbjct: 181 KVHAVDAVVAPDKLQAAALDLVKRAISGELDYKAKRQPKLDKLKLNAIEQMMAFETSKAF 240

Query: 241 VAGQAGPNYPAPVEAIKSIQKAANFGRDKALEVEAAGFVKLAKTSVAQSLIGLFLNDQEL 300
           VAGQAGPNYPAPVEAIK+IQKAANF RDKA+EVEAAGFVKLAKTSVAQSL+GLFL+DQEL
Sbjct: 241 VAGQAGPNYPAPVEAIKTIQKAANFTRDKAIEVEAAGFVKLAKTSVAQSLVGLFLSDQEL 300

Query: 301 KKKAKKYDEVAKDVKLAAVLGAGIMGGGIAYQSALKGTPILMKDIREEGIQMGLNEAAKL 360
           KKKAK YD+ A+DVKLAAVLGAGIMGGGIAYQSA+KGTPILMKDIREEGIQMGL+EA+KL
Sbjct: 301 KKKAKAYDKQARDVKLAAVLGAGIMGGGIAYQSAVKGTPILMKDIREEGIQMGLDEASKL 360

Query: 361 LGKRVEKGRLTPAKMAEALNGIRPTMSYGDFGNVDIVVEAVVENPKVKQAVLAEVEGAVK 420
           LGKRVEKGRLT  KMA+ALN IRPTMSYGDFGNVDIVVEAVVENPKVK AVLAEVEG V+
Sbjct: 361 LGKRVEKGRLTADKMAQALNAIRPTMSYGDFGNVDIVVEAVVENPKVKHAVLAEVEGHVR 420

Query: 421 EDAIIASNTSTISISLLAQALKRPENFCGMHFFNPVHMMPLVEVIRGEKTGETAIATTVA 480
           EDAIIASNTSTISI+ LAQALKRPENFCGMHFFNPVHMMPLVEVIRGEKT E AIATTVA
Sbjct: 421 EDAIIASNTSTISINYLAQALKRPENFCGMHFFNPVHMMPLVEVIRGEKTSEVAIATTVA 480

Query: 481 YAKKMGKSPIVVNDCPGFLVNRVLFPYFGGFAKLLSFGVDFVRIDKVMEKFGWPMGPAYL 540
           YAKKMGKSP+VVNDCPGFLVNRVLFPYFGGFA+ ++ GVDFVR DKVMEKFGWPMGPAYL
Sbjct: 481 YAKKMGKSPVVVNDCPGFLVNRVLFPYFGGFARAIAHGVDFVRADKVMEKFGWPMGPAYL 540

Query: 541 SDVVGIDTGHHGRDVMAEGFPDRMAVEGKTAVDVMYEANRLGQKNGKGFYAYETDKRGKP 600
            DVVG+DTGHHGRDVMAEGFPDRM  + +TAVDVMYEANRLGQKNGKGFYAYE DK+GKP
Sbjct: 541 MDVVGMDTGHHGRDVMAEGFPDRMKDDTRTAVDVMYEANRLGQKNGKGFYAYEMDKKGKP 600

Query: 601 KKVTDPQAYEVLKPIVVEQREVTDEDIVNFMMIPLCLETVRCLEDGIVETAAEADMGLIY 660
           KKV D QAYE+LKPIV E RE++DEDI+N+MMIPLCLETVRCLEDGIVETAAEADMGLIY
Sbjct: 601 KKVVDAQAYELLKPIVAETRELSDEDIINYMMIPLCLETVRCLEDGIVETAAEADMGLIY 660

Query: 661 GIGFPPFRGGALRYIDSIGVAEFVALADKYAELGALYHPTAKLREMAKNGQKFFG 715
           GIGFPPFRGGALRYIDSIGVAEFVA+ADKYA+LG LYHPTAKLREMA NGQ+F+G
Sbjct: 661 GIGFPPFRGGALRYIDSIGVAEFVAMADKYADLGPLYHPTAKLREMAANGQRFYG 715


Lambda     K      H
   0.318    0.137    0.388 

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: 1574
Number of extensions: 57
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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