Alignments for a candidate for fadB in Brevibacterium jeotgali SJ5-8

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Brevibacterium jeotgali SJ5-8

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_101589956.1 BJEO58_RS13310 3-hydroxyacyl-CoA dehydrogenase

Query= reanno::BFirm:BPHYT_RS13545
         (706 letters)



>NCBI__GCF_900169175.1:WP_101589956.1
          Length = 702

 Score =  569 bits (1467), Expect = e-166
 Identities = 311/704 (44%), Positives = 441/704 (62%), Gaps = 20/704 (2%)

Query: 8   DVVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAG 67
           DVV+ E+   + +VT+D  PVNALS  VR GL  A  AA+AD A +A++++ AGR FIAG
Sbjct: 6   DVVTLEIEEGIAVVTLDSPPVNALSQAVRSGLRDAFAAANADDAAKAIVLICAGRTFIAG 65

Query: 68  ADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLG 127
           ADI EFG      +   + + ++   KPV+AAIHG ALGGGLEVAL+ HYR+A   AK+G
Sbjct: 66  ADISEFGSDAPKDTGASIFSVLDDSPKPVIAAIHGTALGGGLEVALSTHYRVATTSAKVG 125

Query: 128 LPEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAE 187
           LPEV LGLLPG GGTQR PRL GA  ALDLI SGRH  A EAL  G+ID + + +D+   
Sbjct: 126 LPEVHLGLLPGGGGTQRLPRLTGAATALDLITSGRHVPAAEALDLGIIDEVVADEDLRGS 185

Query: 188 GLAYVHELLAAHAPVRRTRD-----AAALSDRAASLAAVATARAETAKKSRGLFSPLKIV 242
            L +  +++ A  P+ R RD     AA   D       +A+      K  RG  +P +IV
Sbjct: 186 TLRFARQIVDAGGPLPRVRDLDEKIAADRDDPELFDRFIASH----PKLFRGFLAPTEIV 241

Query: 243 DAVEAAIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRT-LN 301
             + AA+ +PFD+G+  E++ F   + S + A   + FFAER   K  +  A  PR  ++
Sbjct: 242 ACIRAAVTRPFDDGMAEEQERFQTLLTSSESAAQRYYFFAERAARKIADVPADTPRIPVS 301

Query: 302 TIGVVGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKK 361
           T+G++G GTMG GIA+    AG+PVT++E+   +L RG A I K Y+   +KGR++  + 
Sbjct: 302 TVGIIGAGTMGGGIAMNFATAGIPVTLVEQKQEALDRGLATIRKNYERTASKGRITTAQV 361

Query: 362 AALMSRWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDID 421
              M+  +GS S D LA  D+VIEAVFE + +K+ VF +LDR+CK GA+LATNTS L++D
Sbjct: 362 EERMALITGSISMDDLATVDMVIEAVFERMDIKKDVFTQLDRICKPGAILATNTSALNVD 421

Query: 422 ALASSVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVC 481
            +A+  SRP  V+G HFFSPAN+MKLLE V  ++ S +V+AT   L++ + K  V  GVC
Sbjct: 422 EIAAVTSRPEYVVGTHFFSPANVMKLLENVRGEKTSKEVIATVMALSRTIGKIAVLVGVC 481

Query: 482 DGFIGNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKR 541
            GF+GNR+L     A++ ++ +GA P+ +D A+  FG PMG +Q+ DLAG DIGW   + 
Sbjct: 482 PGFVGNRILYARSRASEQLVMEGAMPWDVDRALTNFGLPMGTYQMSDLAGLDIGWVKGEP 541

Query: 542 RAATRNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAG 601
            A           I D LCE    GQK+G GFY Y E +R+ TP P    I++ +RA+AG
Sbjct: 542 TA---------YPIKDALCEMDRRGQKTGAGFYDYDE-NRTATPSPITAQIVEDQRAKAG 591

Query: 602 ITPRSFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYAD 661
           +TPR  ++EEI+ R +  M+NEG  ++ E +A R  D+DV ++ GYG+P YRGGPM YA+
Sbjct: 592 VTPREISEEEILERTLLPMVNEGFKILQEGMAERASDIDVVYVNGYGWPVYRGGPMFYAE 651

Query: 662 MVGLPKILADIREFAKEDPLFWKPSPLLIELVERGADFASLNQS 705
            +G   +L  +R +A+     + P+ LL  +V +G   ++L ++
Sbjct: 652 QLGAETVLEKLRGYAERLGEDFAPAALLEAVVAKGQKISTLTKA 695


Lambda     K      H
   0.320    0.136    0.392 

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: 1052
Number of extensions: 48
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 706
Length of database: 702
Length adjustment: 39
Effective length of query: 667
Effective length of database: 663
Effective search space:   442221
Effective search space used:   442221
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: 54 (25.4 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