Alignments for a candidate for fadB in Photobacterium jeanii R-40508

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Photobacterium jeanii R-40508

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 WP_068334218.1 A3K86_RS17390 fatty acid oxidation complex subunit alpha FadB

Query= SwissProt::P21177
         (729 letters)



>NCBI__GCF_001650345.1:WP_068334218.1
          Length = 725

 Score =  994 bits (2570), Expect = 0.0
 Identities = 493/715 (68%), Positives = 586/715 (81%)

Query: 1   MLYKGDTLYLDWLEDGIAELVFDAPGSVNKLDTATVASLGEAIGVLEQQSDLKGLLLRSN 60
           M+Y+GDTL + +LEDGIAEL  +AP S+NK D  T+  L EA+  L QQ+DLKGL+L S 
Sbjct: 1   MIYQGDTLSVRYLEDGIAELNLNAPSSINKFDIKTLTCLSEALNALYQQTDLKGLILTSA 60

Query: 61  KAAFIVGADITEFLSLFLVPEEQLSQWLHFANSVFNRLEDLPVPTIAAVNGYALGGGCEC 120
           K AFIVGADITEFL LF   E +LSQWL  AN +FN+LEDLPVPT++A+NG+ALGGGCEC
Sbjct: 61  KDAFIVGADITEFLGLFAQTEAELSQWLTRANDIFNKLEDLPVPTLSAINGHALGGGCEC 120

Query: 121 VLATDYRLATPDLRIGLPETKLGIMPGFGGSVRMPRMLGADSALEIIAAGKDVGADQALK 180
           VLATD+RLA    RIGLPETKLGIMPGFGG+VR+PR++GADSA+EII AGKD  A  ALK
Sbjct: 121 VLATDFRLADTTARIGLPETKLGIMPGFGGTVRLPRLIGADSAMEIITAGKDKKAQDALK 180

Query: 181 IGLVDGVVKAEKLVEGAKAVLRQAINGDLDWKAKRQPKLEPLKLSKIEATMSFTIAKGMV 240
           +G+VD VV  E+L + A A+++ AI+G L+W+ +R  K  PL+L++ EATMSFT+AK MV
Sbjct: 181 LGMVDAVVAPEQLRDAAIAMIKDAIDGKLNWQQRRAQKQAPLQLNRTEATMSFTMAKAMV 240

Query: 241 AQTAGKHYPAPITAVKTIEAAARFGREEALNLENKSFVPLAHTNEARALVGIFLNDQYVK 300
           A+ AGKHYPAP+TAV TIE A R+ R+EAL +ENK FV LA T  A+ALVG+FLNDQ++K
Sbjct: 241 AKVAGKHYPAPMTAVVTIEEATRYQRDEALQVENKHFVTLAKTEVAQALVGLFLNDQHIK 300

Query: 301 GKAKKLTKDVETPKQAAVLGAGIMGGGIAYQSAWKGVPVVMKDINDKSLTLGMTEAAKLL 360
           G+AK+  K  +   + AVLGAGIMGGGIAYQSA KGVPV+MKDI + SL LGMTEA KLL
Sbjct: 301 GQAKQAAKAGKATHKGAVLGAGIMGGGIAYQSALKGVPVLMKDIAEPSLELGMTEATKLL 360

Query: 361 NKQLERGKIDGLKLAGVISTIHPTLDYAGFDRVDIVVEAVVENPKVKKAVLAETEQKVRQ 420
           NKQLERG+IDG K+A VIS I P+L+YAG +  D+VVEAVVENPK+K AVL E EQ V  
Sbjct: 361 NKQLERGRIDGFKMAKVISAITPSLNYAGIEHADVVVEAVVENPKIKAAVLNEVEQHVSP 420

Query: 421 DTVLASNTSTIPISELANALERPENFCGMHFFNPVHRMPLVEIIRGEKSSDETIAKVVAW 480
           + V+ SNTSTIPI+ LA +LERPENFCGMHFFNPVHRMPLVEIIRG+K+S++TI +VVA+
Sbjct: 421 EAVITSNTSTIPINLLAQSLERPENFCGMHFFNPVHRMPLVEIIRGDKTSEDTINRVVAY 480

Query: 481 ASKMGKTPIVVNDCPGFFVNRVLFPYFAGFSQLLRDGADFRKIDKVMEKQFGWPMGPAYL 540
           A+KMGK+PIVVNDCPGFFVNRVLFPYFAGFS LLRDGADF++IDKVMEKQFGWPMGPAYL
Sbjct: 481 AAKMGKSPIVVNDCPGFFVNRVLFPYFAGFSMLLRDGADFQQIDKVMEKQFGWPMGPAYL 540

Query: 541 LDVVGIDTAHHAQAVMAAGFPQRMQKDYRDAIDALFDANRFGQKNGLGFWRYKEDSKGKP 600
           LDVVGIDTAHHAQAVMA GFP+RM KDY+DA+D +F+  R+GQKNG GF+ Y  D KGKP
Sbjct: 541 LDVVGIDTAHHAQAVMAEGFPERMNKDYKDAVDVMFENQRYGQKNGHGFYAYTLDRKGKP 600

Query: 601 KKEEDAAVEDLLAEVSQPKRDFSEEEIIARMMIPMVNEVVRCLEEGIIATPAEADMALVY 660
           KK  D  V +LL+ V+    D+S E IIAR M+PM+NEVVRCLEEGIIA+PA+ADMALVY
Sbjct: 601 KKAADPEVANLLSTVNGTATDYSSEAIIARTMVPMINEVVRCLEEGIIASPADADMALVY 660

Query: 661 GLGFPPFHGGAFRWLDTLGSAKYLDMAQQYQHLGPLYEVPEGLRNKARHNEPYYP 715
           GLGFPPF GG FR+LDTLG A Y+ MA QY HLG +Y+VP GLR KA   E YYP
Sbjct: 661 GLGFPPFRGGVFRYLDTLGLANYVAMADQYAHLGAVYQVPAGLREKASKGETYYP 715


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: 1387
Number of extensions: 48
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: 725
Length adjustment: 40
Effective length of query: 689
Effective length of database: 685
Effective search space:   471965
Effective search space used:   471965
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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Protein sequences (fasta format)
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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 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