GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Klebsiella michiganensis M5al

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 BWI76_RS01365 BWI76_RS01365 multifunctional fatty acid oxidation complex subunit alpha

Query= SwissProt::P21177
         (729 letters)



>FitnessBrowser__Koxy:BWI76_RS01365
          Length = 729

 Score = 1374 bits (3557), Expect = 0.0
 Identities = 683/729 (93%), Positives = 710/729 (97%)

Query: 1   MLYKGDTLYLDWLEDGIAELVFDAPGSVNKLDTATVASLGEAIGVLEQQSDLKGLLLRSN 60
           MLYKGDTLYLDW EDGIAELVFDAPGSVNKLDTATVASLGEA+ VLE+Q DLKGLLLRS 
Sbjct: 1   MLYKGDTLYLDWREDGIAELVFDAPGSVNKLDTATVASLGEALDVLEKQKDLKGLLLRSE 60

Query: 61  KAAFIVGADITEFLSLFLVPEEQLSQWLHFANSVFNRLEDLPVPTIAAVNGYALGGGCEC 120
           KAAFIVGADITEFLSLFLVPEEQLSQWLHFANSVFNRLEDLPVPTI+AVNGYALGGGCEC
Sbjct: 61  KAAFIVGADITEFLSLFLVPEEQLSQWLHFANSVFNRLEDLPVPTISAVNGYALGGGCEC 120

Query: 121 VLATDYRLATPDLRIGLPETKLGIMPGFGGSVRMPRMLGADSALEIIAAGKDVGADQALK 180
           VLATDYRLATPDLRIGLPETKLGIMPGFGGSVRMPRMLGADSALEIIAAGKD+GA+QALK
Sbjct: 121 VLATDYRLATPDLRIGLPETKLGIMPGFGGSVRMPRMLGADSALEIIAAGKDLGAEQALK 180

Query: 181 IGLVDGVVKAEKLVEGAKAVLRQAINGDLDWKAKRQPKLEPLKLSKIEATMSFTIAKGMV 240
           IGLVDGVVK EKL++GA A+LRQAINGDLDWKAKRQPKLEPL LSKIEA MSFTIAKGMV
Sbjct: 181 IGLVDGVVKHEKLIDGAVAILRQAINGDLDWKAKRQPKLEPLHLSKIEAAMSFTIAKGMV 240

Query: 241 AQTAGKHYPAPITAVKTIEAAARFGREEALNLENKSFVPLAHTNEARALVGIFLNDQYVK 300
           AQTAGKHYPAP+TAVKTIEAAARFGREEALNLENKSFVPLAHTNEARALVGIFLNDQYVK
Sbjct: 241 AQTAGKHYPAPLTAVKTIEAAARFGREEALNLENKSFVPLAHTNEARALVGIFLNDQYVK 300

Query: 301 GKAKKLTKDVETPKQAAVLGAGIMGGGIAYQSAWKGVPVVMKDINDKSLTLGMTEAAKLL 360
            KAKKLTKDV+TPK AAVLGAGIMGGGIAYQSAWKGVPVVMKDINDKSLTLGMTEAAKLL
Sbjct: 301 AKAKKLTKDVDTPKHAAVLGAGIMGGGIAYQSAWKGVPVVMKDINDKSLTLGMTEAAKLL 360

Query: 361 NKQLERGKIDGLKLAGVISTIHPTLDYAGFDRVDIVVEAVVENPKVKKAVLAETEQKVRQ 420
           NKQLERGKIDGLK+AGVISTI PTLDYAGF+RVD+VVEAVVENPKVKKAVLAETE+KVR 
Sbjct: 361 NKQLERGKIDGLKMAGVISTIQPTLDYAGFERVDVVVEAVVENPKVKKAVLAETEEKVRP 420

Query: 421 DTVLASNTSTIPISELANALERPENFCGMHFFNPVHRMPLVEIIRGEKSSDETIAKVVAW 480
           DTVLASNTSTIPISELA+ L+RPENFCGMHFFNPVHRMPLVE+IRG+K+SD+TIAKVVAW
Sbjct: 421 DTVLASNTSTIPISELASVLQRPENFCGMHFFNPVHRMPLVEVIRGDKTSDKTIAKVVAW 480

Query: 481 ASKMGKTPIVVNDCPGFFVNRVLFPYFAGFSQLLRDGADFRKIDKVMEKQFGWPMGPAYL 540
           ASKMGKTPIVVNDCPGFFVNRVLFPYFAGFSQLLRDGADFRK+DKVMEKQFGWPMGPAYL
Sbjct: 481 ASKMGKTPIVVNDCPGFFVNRVLFPYFAGFSQLLRDGADFRKVDKVMEKQFGWPMGPAYL 540

Query: 541 LDVVGIDTAHHAQAVMAAGFPQRMQKDYRDAIDALFDANRFGQKNGLGFWRYKEDSKGKP 600
           LDVVGIDTAHHAQAVMAAGFPQRMQK+YRDAIDALFDA RFGQKNGLGFWRYKEDSKGKP
Sbjct: 541 LDVVGIDTAHHAQAVMAAGFPQRMQKEYRDAIDALFDAKRFGQKNGLGFWRYKEDSKGKP 600

Query: 601 KKEEDAAVEDLLAEVSQPKRDFSEEEIIARMMIPMVNEVVRCLEEGIIATPAEADMALVY 660
           KKEED  V+ LLAEVSQPKRDFS+EEIIARMMIPMVNEVVRCLEEGIIA+PAEADMALVY
Sbjct: 601 KKEEDTVVDSLLAEVSQPKRDFSDEEIIARMMIPMVNEVVRCLEEGIIASPAEADMALVY 660

Query: 661 GLGFPPFHGGAFRWLDTLGSAKYLDMAQQYQHLGPLYEVPEGLRNKARHNEPYYPPVEPA 720
           GLGFPPFHGGAFRWLDTLGSAKYLDMAQQYQHLGPLY+VPEGLR+KARHNEPYYPPVEPA
Sbjct: 661 GLGFPPFHGGAFRWLDTLGSAKYLDMAQQYQHLGPLYDVPEGLRSKARHNEPYYPPVEPA 720

Query: 721 RPVGDLKTA 729
           R  GDLKTA
Sbjct: 721 RAPGDLKTA 729


Lambda     K      H
   0.318    0.136    0.399 

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: 1746
Number of extensions: 54
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: 729
Length of database: 729
Length adjustment: 40
Effective length of query: 689
Effective length of database: 689
Effective search space:   474721
Effective search space used:   474721
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