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

GapMind for catabolism of small carbon sources

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

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate WP_101589956.1 BJEO58_RS13310 3-hydroxyacyl-CoA dehydrogenase

Query= metacyc::MONOMER-20678
         (699 letters)



>NCBI__GCF_900169175.1:WP_101589956.1
          Length = 702

 Score =  692 bits (1787), Expect = 0.0
 Identities = 363/699 (51%), Positives = 484/699 (69%), Gaps = 6/699 (0%)

Query: 2   SEVVTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIA 61
           ++VVT   ++ +A+VT+DSPPVNALS AVR G+ +   AA AD A +AIVL+CAGRTFIA
Sbjct: 5   NDVVTLEIEEGIAVVTLDSPPVNALSQAVRSGLRDAFAAANADDAAKAIVLICAGRTFIA 64

Query: 62  GADITEFGKPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKL 121
           GADI+EFG          + + L++SPKP IAAIHGTALGGGLEVAL  H+RVA   AK+
Sbjct: 65  GADISEFGSDAPKDTGASIFSVLDDSPKPVIAAIHGTALGGGLEVALSTHYRVATTSAKV 124

Query: 122 GLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVV--ENLVA 179
           GLPEV LGLLPG GGTQRLPR  G   A+ +I  G  + AAEAL  G+++EVV  E+L  
Sbjct: 125 GLPEVHLGLLPGGGGTQRLPRLTGAATALDLITSGRHVPAAEALDLGIIDEVVADEDLRG 184

Query: 180 GAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAI 239
             + FA++++    PL R+RD D K+AA + D  +F   +A+  K  RG  AP      I
Sbjct: 185 STLRFARQIVDAGGPLPRVRDLDEKIAADRDDPELFDRFIASHPKLFRGFLAPTEIVACI 244

Query: 240 GAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVA 299
            AA+  PF++G+ +E+E F  L+ S +S AQRY FFAER A K+  VP  T   PVS V 
Sbjct: 245 RAAVTRPFDDGMAEEQERFQTLLTSSESAAQRYYFFAERAARKIADVPADTPRIPVSTVG 304

Query: 300 IIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKR 359
           IIGAGTMGGGIAM+FA AGIPVTL+E  +E L RGL  ++KN+E TA++G +      +R
Sbjct: 305 IIGAGTMGGGIAMNFATAGIPVTLVEQKQEALDRGLATIRKNYERTASKGRITTAQVEER 364

Query: 360 MALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIA 419
           MALITG + ++++   D++IEAVFE M +KK+VFT +D   KPGA+LA+NTS L++DEIA
Sbjct: 365 MALITGSISMDDLATVDMVIEAVFERMDIKKDVFTQLDRICKPGAILATNTSALNVDEIA 424

Query: 420 ATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGF 479
           A T RP+ V+G HFFSPANVMKL E VRG KT+ + + T +++++ I K+ V+VGVC GF
Sbjct: 425 AVTSRPEYVVGTHFFSPANVMKLLENVRGEKTSKEVIATVMALSRTIGKIAVLVGVCPGF 484

Query: 480 VGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRGI 539
           VGNR+L ARS+ SE+L+ EGA+P  VD  +T FG+PMG + M DLAGLDIGW   K    
Sbjct: 485 VGNRILYARSRASEQLVMEGAMPWDVDRALTNFGLPMGTYQMSDLAGLDIGW--VKGEPT 542

Query: 540 KSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDEE 599
              I DALCE  R GQKTG G+Y Y++ +R   P P    ++ D  AK G+  R+I++EE
Sbjct: 543 AYPIKDALCEMDRRGQKTGAGFYDYDE-NRTATPSPITAQIVEDQRAKAGVTPREISEEE 601

Query: 600 ILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAER 659
           ILER + PM+NEG +IL+E +A R SDIDVV++ GYGWP+YRGGPM YA+ +G + + E+
Sbjct: 602 ILERTLLPMVNEGFKILQEGMAERASDIDVVYVNGYGWPVYRGGPMFYAEQLGAETVLEK 661

Query: 660 LSAYAKATNDPSLEPAPLLARLAAEGKTFASLTQPSKAA 698
           L  YA+   +    PA LL  + A+G+  ++LT+   A+
Sbjct: 662 LRGYAERLGE-DFAPAALLEAVVAKGQKISTLTKADAAS 699


Lambda     K      H
   0.317    0.134    0.383 

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: 1091
Number of extensions: 48
Number of successful extensions: 4
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: 699
Length of database: 702
Length adjustment: 39
Effective length of query: 660
Effective length of database: 663
Effective search space:   437580
Effective search space used:   437580
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: 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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