Alignments for a candidate for fadB in Amphritea japonica JAMM 1866

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Amphritea japonica JAMM 1866

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_019620070.1 G329_RS0100985 fatty acid oxidation complex subunit alpha FadB

Query= SwissProt::P28793
         (715 letters)



>NCBI__GCF_000381785.1:WP_019620070.1
          Length = 714

 Score =  669 bits (1727), Expect = 0.0
 Identities = 357/715 (49%), Positives = 473/715 (66%), Gaps = 3/715 (0%)

Query: 2   IYEGKAITVTALESGIVELKFDLKGESVNKFNRLTLNELRQAVDAIKADASVKGVIVSSG 61
           +Y G  + V AL++G++EL FD++  SVN FN  T+ EL  A++ I+    +KG++V+S 
Sbjct: 1   MYIGSKLNVKALDNGLIELSFDVRDGSVNVFNNETVVELSAALEVIEKAEGIKGMLVTSA 60

Query: 62  KDVFIVGADITEFVENFKLPDAELIAGNLEANKIFSDFEDLNVPTVAAINGIALGGGLEM 121
           K  FIVGADI+EF E F L + ++ +     N  FS  E L+ P V AING ALGGGLE 
Sbjct: 61  KSDFIVGADISEFKEIFSLSEEQIKSRIAINNTNFSRLESLSFPVVVAINGFALGGGLEF 120

Query: 122 CLAADFRVMADSAKIGLPEVKLGIYPGFGGTVRLPRLIGVDNAVEWIASGKENRAEDALK 181
           CLA D+RVM+D A I LPE  LGI PG+GGTVR PRL+G++ A++W+ASG   +A  AL+
Sbjct: 121 CLACDYRVMSDKAVISLPETGLGILPGWGGTVRTPRLVGLETALQWVASGAPQKAPVALE 180

Query: 182 VSAVDAVVTADKLGAAALDLIKRAISGELDYKAKRQPKLEKLKLNAIEQMMAFETAKGFV 241
              V  V   ++L   AL+L+  AI    + +  R  K   L +++ E     +  KG V
Sbjct: 181 SGLVSKVAEVNELRQVALELLNYAIDHSEEVQIGRIAKASALSISSEEAQQLAQAVKGKV 240

Query: 242 AGQAGPNYPAPVEAIKTIQKAANFGRDKALEVEAAGFAKLAKTSASNCLIGLFLNDQELK 301
             +  P   AP  AI  I +A+    DKALE EA   A LA TS S  LIG F+NDQ +K
Sbjct: 241 CAR-NPQLLAPAAAIDLIAEASQLSSDKALEKEANVCAALATTSQSRALIGNFMNDQYIK 299

Query: 302 KKAKVYDKIAK-DVKQAAVLGAGIMGGGIAYQSASKGTPILMKDINEHGIEQGLAEAAKL 360
           K A+ Y K AK  + +  V+GAGIMGGGIAYQ+A KG  ++MKDI E  ++ G+ EA KL
Sbjct: 300 KVARAYAKDAKLTLDKTTVVGAGIMGGGIAYQNALKGIKVVMKDIGESALDLGMTEADKL 359

Query: 361 LVGRVDKGRMTPAKMAEVLNGIRPTLSYGDFGNVDLVVEAVVENPKVKQAVLAEVENHVR 420
           L  RV  GRMT  K A++L  I PTL   D     ++VEAVVENPKVK+AVLAE+EN++ 
Sbjct: 360 LSKRVRLGRMTEGKKADILKAITPTLEASDMDRSKVIVEAVVENPKVKEAVLAELENNLA 419

Query: 421 EDAILASNTSTISISLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSDLAVATTVA 480
           E  +L SNTSTISI+ LA+ALKRP+ F G+HFFNPVH MPLVEV+R E+SSD  ++  VA
Sbjct: 420 EGGVLVSNTSTISITRLARALKRPDQFAGLHFFNPVHAMPLVEVVRAEQSSDQTISDLVA 479

Query: 481 YAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYL 540
           Y   +GK PIVVNDCP FLVNRVLFPYF GF +L++ G DF RID+VM+ +GWPMGPAYL
Sbjct: 480 YTLALGKQPIVVNDCPAFLVNRVLFPYFRGFEQLINDGGDFQRIDQVMQAWGWPMGPAYL 539

Query: 541 MDVVGIDTGHHGRDVMAEGFPDRMKDDRRSAIDALYEAKRLGQKNGKGFYAYEADKKGKQ 600
            DV+GIDT  H  DV+A+ FPDRM    +S ++ +  A+R GQKNGKGFY Y  D KG+ 
Sbjct: 540 SDVIGIDTLCHCIDVLAQDFPDRMAQLDKSILNDMNTAERFGQKNGKGFYQYLPDAKGRP 599

Query: 601 KKLVDSSVLEVLKPIVYEQRDVTDEDIINWMMIPLCLETVRCLEDGIVETAAEADMGLVY 660
           +K VD +   ++      + D+TDE+I    M+P+ +E  RCLE+GIV++ AEADM L+ 
Sbjct: 600 QKSVDDTTSSMIAQCQSAKVDLTDEEIEFRCMLPMAIEMARCLEEGIVDSPAEADMALLM 659

Query: 661 GIGFPLFRGGALRYIDSIGVAEFVALADQYAE-LGALYHPTAKLREMAKNGQSFF 714
           G+GFP FRGG +R++D +G+       D+ A  LG  Y PTA +R MA +  S++
Sbjct: 660 GLGFPAFRGGVVRWMDEVGMTALCQWGDRLASTLGEAYRPTANMRIMAADSISYY 714


Lambda     K      H
   0.318    0.137    0.386 

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: 1182
Number of extensions: 61
Number of successful extensions: 3
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: 714
Length adjustment: 39
Effective length of query: 676
Effective length of database: 675
Effective search space:   456300
Effective search space used:   456300
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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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