Alignments for a candidate for pimF in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pimF in Paraburkholderia bryophila 376MFSha3.1

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate H281DRAFT_00361 H281DRAFT_00361 short chain enoyl-CoA hydratase /3-hydroxyacyl-CoA dehydrogenase

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



>FitnessBrowser__Burk376:H281DRAFT_00361
          Length = 706

 Score =  651 bits (1680), Expect = 0.0
 Identities = 351/704 (49%), Positives = 468/704 (66%), Gaps = 22/704 (3%)

Query: 2   SEVVTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIA 61
           ++VVTR  + +V +VT+D  PVNALSA VRRG+L  + AA +DP+VQA+++V AGR FIA
Sbjct: 7   TDVVTRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADSDPSVQAVLIVGAGRNFIA 66

Query: 62  GADITEFGKPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKL 121
           GADI EFGKPP PP+L DV   +E   KP +AAIHG ALGGGLEVAL  H+R+AV  AKL
Sbjct: 67  GADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRLAVDGAKL 126

Query: 122 GLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEV--VENLVA 179
           GLPEV+LGLLPGAGGTQR PR +G + A+ +++ G    A EAL  GLV+ +   ++++A
Sbjct: 127 GLPEVQLGLLPGAGGTQRTPRLIGAQAALDLMLSGRHANAQEALALGLVDRLGSSDDILA 186

Query: 180 GAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAM----TKKARGLEAPFAC 235
             +A+  ++LA   P+RR RD     A A  DR+    AVA       KK+RGL +P   
Sbjct: 187 EGLAYVHELLAGHAPVRRTRD-----ATALNDRASSLAAVATARAETAKKSRGLFSPLKI 241

Query: 236 ADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPV 295
            DA+ AAI  PFE+GL++ER+ F++ + S Q     +AFFAERE  K     D TKPR +
Sbjct: 242 VDAVEAAIAQPFEDGLRRERQLFLECLDSPQRAGLVHAFFAEREVLKAPETRD-TKPRAL 300

Query: 296 SRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDA 355
           + + ++G GTMG GIA++  +AG+PVT+IE  E  L RG   ++K ++   A+G +  + 
Sbjct: 301 NAIGVVGGGTMGAGIAVAVLDAGLPVTMIERDEASLARGRAHIEKVYDGLIAKGRMSAEK 360

Query: 356 PAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSI 415
            A+ MA  TG    + + DADL+IEAVFE ++VK+ VF  +D   KPGAVLA+NTSYL I
Sbjct: 361 KAQLMARWTGSTSYDALADADLVIEAVFEDLSVKQAVFAELDRVCKPGAVLATNTSYLDI 420

Query: 416 DEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGV 475
           D IAA+  RP DV+G+HFFSPAN+MKL E+V     + D + TA  +AKK+ K PV  GV
Sbjct: 421 DAIAASISRPADVIGLHFFSPANIMKLLEVVVPKAVSADVVATAFELAKKLRKTPVRAGV 480

Query: 476 CDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRK 535
           CDGF+GNR+LA     ++ ++ +GA P Q+DA V  FG PMGPF + DLAG DIGW +RK
Sbjct: 481 CDGFIGNRILAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARK 540

Query: 536 DRGIKS-------EIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKL 588
            R           +IAD LCE G FGQKTG+G+Y Y +GSR+  PDPEVE +I+    + 
Sbjct: 541 RRAATRNPAARYVQIADRLCERGWFGQKTGRGFYLYPEGSRSGQPDPEVEAIIDAERVRA 600

Query: 589 GLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYA 648
           G+  R+ +D+EI+ R +  MINEGA ++ E+IA RP D+DV +LYGYG+P YRGGPM YA
Sbjct: 601 GITPREFSDDEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYA 660

Query: 649 DSVGLKHIAERLSAYAKATNDPSL-EPAPLLARLAAEGKTFASL 691
           D +GL  I   +  +AK   DP     +PLL  L   G  FASL
Sbjct: 661 DMIGLPRILADIREFAK--EDPLFWRASPLLIDLVERGADFASL 702


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: 1202
Number of extensions: 57
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: 706
Length adjustment: 39
Effective length of query: 660
Effective length of database: 667
Effective search space:   440220
Effective search space used:   440220
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 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:

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 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