GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Burk376:H281DRAFT_00361 H281DRAFT_00361 short
           chain enoyl-CoA hydratase /3-hydroxyacyl-CoA
           dehydrogenase
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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