GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Halioglobus japonicus S1-36

Align fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized)
to candidate WP_084198637.1 C0029_RS18685 fatty acid oxidation complex subunit alpha FadB

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



>NCBI__GCF_002869505.1:WP_084198637.1
          Length = 715

 Score =  835 bits (2158), Expect = 0.0
 Identities = 422/715 (59%), Positives = 529/715 (73%), Gaps = 1/715 (0%)

Query: 1   MIYQGKAITVKPLEGGIVELNFDLKGESVNKFNRLTLSELRAAVDAIKADASVKGVIVTS 60
           MIYQ   +T+K LEG I ELNFDL+GESVNKF++ T++ L A +DA++A++ +KG++VTS
Sbjct: 1   MIYQSDQLTIKRLEGDIAELNFDLQGESVNKFDQATVASLTAGLDALEAESGIKGLLVTS 60

Query: 61  GKDVFIVGADITEFVDNFQLPDEELMAGNLEANKIFSDFEDLDVPTVAAINGIALGGGLE 120
           GK VFIVGADITEFV  F    EE+       N  F+    L  P+  AING A+GGGLE
Sbjct: 61  GKPVFIVGADITEFVQLFGSSKEEIKPFTGINNANFNRLAALPYPSAVAINGFAMGGGLE 120

Query: 121 MCLAADFRVMSATAKVGLPEVKLGIYPGFGGTVRLPRLIGCDNAVEWIASGKENKAEDAL 180
           +CLA DFR+MS  AKVGLPE KLGI PG+GGTVRLPR+IG D AV W+A+G + + + AL
Sbjct: 121 ICLACDFRIMSTAAKVGLPETKLGILPGWGGTVRLPRIIGVDEAVMWMATGADKRPDAAL 180

Query: 181 KVGAVDAVVAPEQLQAAALDLAKRAVAGELDHKARRQPKLEKLKLNAIEQMMAFETAKGF 240
           K GAVDAV APEQL+  AL     A+ G LD+K RR  K   L LN IE MM+F T K  
Sbjct: 181 KAGAVDAVAAPEQLREVALTTLNNAIEGGLDYKGRRAQKHGPLPLNDIEAMMSFFTIKSM 240

Query: 241 VAGQAGPNYPAPVEAIKSIQKAANFGRDKALEVEAAGFVKLAKTSVAQSLIGLFLNDQEL 300
           V  QAG NYPAP++ +  I++A +   + AL+VEA GF +LA T VA +L+G+FLNDQ L
Sbjct: 241 VGQQAGKNYPAPLKVVDVIEQARSMSLEDALDVEAEGFAELATTPVAAALVGVFLNDQLL 300

Query: 301 KKKAKKYDEVA-KDVKLAAVLGAGIMGGGIAYQSALKGTPILMKDIREEGIQMGLNEAAK 359
            K AK +++ A K ++ AAVLGAGIMGGGIAYQSALKGTPI MKDI ++G+ +GL+EA K
Sbjct: 301 GKVAKGWEKQADKKIENAAVLGAGIMGGGIAYQSALKGTPIKMKDINQDGLDLGLSEANK 360

Query: 360 LLGKRVEKGRLTPAKMAEALNGIRPTMSYGDFGNVDIVVEAVVENPKVKQAVLAEVEGAV 419
           LL KRV KGR+T   M + LN I PT++Y  F  VDIVVEAVVEN KVK  VLAE E  +
Sbjct: 361 LLAKRVAKGRMTADTMGDILNSIDPTLTYAGFDGVDIVVEAVVENEKVKGIVLAETEKEI 420

Query: 420 KEDAIIASNTSTISISLLAQALKRPENFCGMHFFNPVHMMPLVEVIRGEKTGETAIATTV 479
            +DA++ASNTSTISI+ LA+ L+RPENFCGMHFFNPVH MPLVEVIRGEKT + AIA TV
Sbjct: 421 DKDAVLASNTSTISITRLAENLERPENFCGMHFFNPVHAMPLVEVIRGEKTSDNAIARTV 480

Query: 480 AYAKKMGKSPIVVNDCPGFLVNRVLFPYFGGFAKLLSFGVDFVRIDKVMEKFGWPMGPAY 539
           AYA KMGK  +VVNDCPGFLVNRVLFPYFGGF  LL  G DF  IDKVME++GWPMGPAY
Sbjct: 481 AYANKMGKKAVVVNDCPGFLVNRVLFPYFGGFNALLRDGADFQAIDKVMERWGWPMGPAY 540

Query: 540 LSDVVGIDTGHHGRDVMAEGFPDRMAVEGKTAVDVMYEANRLGQKNGKGFYAYETDKRGK 599
           L DVVGIDTG H  +VMAEGFPDRM  + K+A +V++E +R GQKNGKG Y Y TDKRGK
Sbjct: 541 LMDVVGIDTGVHAANVMAEGFPDRMQPDFKSATEVLFENDRYGQKNGKGMYEYVTDKRGK 600

Query: 600 PKKVTDPQAYEVLKPIVVEQREVTDEDIVNFMMIPLCLETVRCLEDGIVETAAEADMGLI 659
           PKKV + + Y+++ P+  E+ E   +DI+  MM+P+ +E  RC+E+GIV T +EAD+ L+
Sbjct: 601 PKKVVNEEVYDLIAPVCGERAEFDKDDIIMRMMLPMAIEMARCVEEGIVGTPSEADLALL 660

Query: 660 YGIGFPPFRGGALRYIDSIGVAEFVALADKYAELGALYHPTAKLREMAKNGQKFF 714
           YG+GFPPFRGG  R++D++G+      + K+A LG  Y  T  +++M  NG+ ++
Sbjct: 661 YGVGFPPFRGGIFRWMDTVGMQAIADASAKFAHLGKAYELTDNMKDMLANGKTYY 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: 1367
Number of extensions: 71
Number of successful extensions: 2
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 24 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