GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Marinobacter adhaerens HP15

Align fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized)
to candidate GFF1550 HP15_1512 multifunctional fatty acid oxidation complex subunit alpha

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



>FitnessBrowser__Marino:GFF1550
          Length = 715

 Score = 1024 bits (2647), Expect = 0.0
 Identities = 507/715 (70%), Positives = 597/715 (83%)

Query: 1   MIYQGKAITVKPLEGGIVELNFDLKGESVNKFNRLTLSELRAAVDAIKADASVKGVIVTS 60
           MIY+GKAITVK +EGGI +LNFDL+GESVNKFNRLT+ ELRAA DA+KA  ++KG++VTS
Sbjct: 1   MIYEGKAITVKEIEGGIAQLNFDLQGESVNKFNRLTIEELRAATDALKAQKNLKGLVVTS 60

Query: 61  GKDVFIVGADITEFVDNFQLPDEELMAGNLEANKIFSDFEDLDVPTVAAINGIALGGGLE 120
            KD FIVGADITEF + F   +E+L+A NL+AN++F+  EDL  PTV AING+ALGGG E
Sbjct: 61  SKDSFIVGADITEFTELFAGSEEDLVANNLKANEVFNAVEDLPFPTVTAINGMALGGGFE 120

Query: 121 MCLAADFRVMSATAKVGLPEVKLGIYPGFGGTVRLPRLIGCDNAVEWIASGKENKAEDAL 180
           MCLA D+RVM   AKVGLPEVKLGI+PGFGGTVRL RL+G DNAVEWI+ G EN+A+ AL
Sbjct: 121 MCLATDYRVMDKKAKVGLPEVKLGIFPGFGGTVRLSRLVGVDNAVEWISGGTENRADVAL 180

Query: 181 KVGAVDAVVAPEQLQAAALDLAKRAVAGELDHKARRQPKLEKLKLNAIEQMMAFETAKGF 240
           KVGAVDAV+  ++L  AA+ +  +   G+LDH+ARR+ K  K+KLNA+E MMAFE +K F
Sbjct: 181 KVGAVDAVLDSDKLVDAAVAIINQCNEGKLDHEARREEKKGKIKLNAMESMMAFEISKAF 240

Query: 241 VAGQAGPNYPAPVEAIKSIQKAANFGRDKALEVEAAGFVKLAKTSVAQSLIGLFLNDQEL 300
           VAG+AG NYPAPVEAIK +QK A   RDKA+EVEA GF K+AKT+VA  L+GLFLNDQEL
Sbjct: 241 VAGKAGKNYPAPVEAIKVMQKHAGMTRDKAIEVEAKGFAKMAKTNVAACLVGLFLNDQEL 300

Query: 301 KKKAKKYDEVAKDVKLAAVLGAGIMGGGIAYQSALKGTPILMKDIREEGIQMGLNEAAKL 360
           KKKAK +++ A DV LAAVLGAGIMGGG+A+QSALKGTPI+MKDI ++GI +GL EA KL
Sbjct: 301 KKKAKAWEKEANDVNLAAVLGAGIMGGGVAFQSALKGTPIIMKDINQDGIALGLKEAKKL 360

Query: 361 LGKRVEKGRLTPAKMAEALNGIRPTMSYGDFGNVDIVVEAVVENPKVKQAVLAEVEGAVK 420
           L KRVEKG++ P +MA+ LN I PT++YGDF NVD+VVEAVVENPKVK AVL E E AV+
Sbjct: 361 LSKRVEKGKMKPDQMADVLNSITPTLNYGDFKNVDLVVEAVVENPKVKDAVLRETEDAVR 420

Query: 421 EDAIIASNTSTISISLLAQALKRPENFCGMHFFNPVHMMPLVEVIRGEKTGETAIATTVA 480
           ED I+ SNTSTISI LLA+ LKRPENFCGMHFFNPVHMMPLVEVIRGEKT + AIATTVA
Sbjct: 421 EDTILTSNTSTISIDLLAKNLKRPENFCGMHFFNPVHMMPLVEVIRGEKTSDRAIATTVA 480

Query: 481 YAKKMGKSPIVVNDCPGFLVNRVLFPYFGGFAKLLSFGVDFVRIDKVMEKFGWPMGPAYL 540
           YAK MGK+PIVVNDCPGFLVNRVLFPYFGGF  L+  G DF  +DKVMEKFGWPMGPAYL
Sbjct: 481 YAKAMGKTPIVVNDCPGFLVNRVLFPYFGGFIGLVRDGADFQHVDKVMEKFGWPMGPAYL 540

Query: 541 SDVVGIDTGHHGRDVMAEGFPDRMAVEGKTAVDVMYEANRLGQKNGKGFYAYETDKRGKP 600
            DVVG+DTG H  +VMA+GFPDRM  EG TA+DVM++ NR GQKN KGFY YE D++GK 
Sbjct: 541 LDVVGMDTGKHAGEVMADGFPDRMKHEGTTAIDVMFDNNRYGQKNDKGFYKYELDRKGKQ 600

Query: 601 KKVTDPQAYEVLKPIVVEQREVTDEDIVNFMMIPLCLETVRCLEDGIVETAAEADMGLIY 660
           KKV D + Y++L+P+V  + E ++EDI+  MMIPLCLETVRCLEDGIVE  A+ADMGLI+
Sbjct: 601 KKVVDEETYKLLEPVVQGKNEFSEEDIIARMMIPLCLETVRCLEDGIVEDPADADMGLIF 660

Query: 661 GIGFPPFRGGALRYIDSIGVAEFVALADKYAELGALYHPTAKLREMAKNGQKFFG 715
           GIGFPPFRGGALRYID +GV +FV LADK+A+LG LYHPT KLREMAK G+KFFG
Sbjct: 661 GIGFPPFRGGALRYIDDMGVDKFVELADKFADLGPLYHPTEKLREMAKTGKKFFG 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: 1461
Number of extensions: 51
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