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 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