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 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