Alignments for a candidate for fadB in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Shewanella oneidensis MR-1

Align fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized)
to candidate 202205 SO3088 fatty oxidation complex, alpha subunit (NCBI ptt file)

Query= CharProtDB::CH_003230
         (714 letters)



>FitnessBrowser__MR1:202205
          Length = 707

 Score =  815 bits (2105), Expect = 0.0
 Identities = 410/710 (57%), Positives = 530/710 (74%), Gaps = 7/710 (0%)

Query: 1   MEMTSAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSA 60
           M +   F L  R D IA++T+DVPGE MNTLKAEF  ++  I+ +++ +  +RG+V +S 
Sbjct: 1   MAVGKTFNLTRREDGIAILTMDVPGETMNTLKAEFGPEISEILSEIKRDSSIRGLVLISG 60

Query: 61  KPDNFIAGADINMIGNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELA 120
           K D+F+AGADI+M+  C+TA +A+AL++QG  +  E+ AL I V+AAIHGACLGGGLELA
Sbjct: 61  KKDSFVAGADISMLDACQTAGDAKALSQQGHVVFNELEALNIPVVAAIHGACLGGGLELA 120

Query: 121 LACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQAL 180
           LACH RVC+DD KT+LG+PEVQLGLLPG GGTQRLPRL+G++TAL+M+LTGKQ+R KQAL
Sbjct: 121 LACHQRVCSDDGKTMLGVPEVQLGLLPGGGGTQRLPRLVGITTALDMMLTGKQIRPKQAL 180

Query: 181 KLGLVDDVVPHSILLEAAVELAKKERPSSRPLP---VRERILAGPLGRALLFKMVGKKTE 237
           K+GLV+DVVP +ILL+ AVE+A   +  ++P+    V + +     GR ++F    K+  
Sbjct: 181 KMGLVNDVVPQTILLQTAVEMALAGKQIAKPVKKSLVNQLLEGTGFGRNIIFDQAAKQVA 240

Query: 238 HKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFASTDVKK 297
            KTQGNYPA  +I++ V  G+A+G   G + EA  F EL ++ +S+ALRSIFFA+T++KK
Sbjct: 241 KKTQGNYPAPAKIIDCVRQGIAKGMQKGLEVEASHFAELVVSKESEALRSIFFATTEMKK 300

Query: 298 DPGSD-APPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQL 356
           + G++ A P  +    ILGGGLMGGGIA VT  KA IP R+KDIN +G+++AL Y++  L
Sbjct: 301 ETGAEGATPRKVKKAVILGGGLMGGGIASVTTTKAKIPARVKDINEKGLSNALSYAYKLL 360

Query: 357 EGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNCAA 416
           +  V+RRH+  + RD  +AL++ TT+Y+G    D+++EAVFE+L LK QMV ++E+ C  
Sbjct: 361 DKGVKRRHMTPAARDNLMALMTTTTEYKGVKDADIVVEAVFEDLALKHQMVKDIERECGE 420

Query: 417 HTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKL 476
           HTIFASNTSSLPIG IA  A+RPE VIGLH+FSPVEKMPLVE+I HA TS +TIATTV  
Sbjct: 421 HTIFASNTSSLPIGQIAQAASRPENVIGLHYFSPVEKMPLVEVIAHAKTSPETIATTVAF 480

Query: 477 AKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLL 536
           A+KQGKTPIVV+D AGFYVNRILA Y+NEA ++L +G+ VEH+D ALVKFGFPVGPI LL
Sbjct: 481 ARKQGKTPIVVQDGAGFYVNRILALYMNEAAQLLLEGQSVEHLDKALVKFGFPVGPITLL 540

Query: 537 DEVGIDTGTKIIPVLEAAYGERFSAPANVVSSILNDDRKGRKNGRGFYLYGQKGRKSKKQ 596
           DEVGID G KI P+LE   GERF APA     +L+DDRKGRKNG+GFY YG   +  KK 
Sbjct: 541 DEVGIDVGAKISPILEKELGERFKAPA-AFDKLLSDDRKGRKNGKGFYQYGAASK--KKA 597

Query: 597 VDPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFGIGFP 656
           VD  +Y ++G +         VAERCV+ MLNEAVRC+D  +I S RDGDIGA+FGIGFP
Sbjct: 598 VDETVYGVLGIKPGVDKEMSAVAERCVVQMLNEAVRCLDAGIIASPRDGDIGAIFGIGFP 657

Query: 657 PFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGESFW 706
           PFLGGPF YID+LGA  +V I++R  TQYG RF PC+RL  M A    F+
Sbjct: 658 PFLGGPFHYIDTLGADNLVKILERYQTQYGDRFEPCQRLKAMAAEKARFF 707


Lambda     K      H
   0.319    0.137    0.393 

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: 1139
Number of extensions: 46
Number of successful extensions: 7
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: 714
Length of database: 707
Length adjustment: 39
Effective length of query: 675
Effective length of database: 668
Effective search space:   450900
Effective search space used:   450900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. 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 2024 update 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