GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimF in Burkholderia phytofirmans PsJN

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate BPHYT_RS13545 BPHYT_RS13545 3-hydroxyacyl-CoA dehydrogenase

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



>FitnessBrowser__BFirm:BPHYT_RS13545
          Length = 706

 Score =  648 bits (1672), Expect = 0.0
 Identities = 349/706 (49%), Positives = 468/706 (66%), Gaps = 22/706 (3%)

Query: 2   SEVVTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIA 61
           ++VV+R  + +V +VT+D  PVNALSA VRRG+L  + AA AD AV+A+++V AGR FIA
Sbjct: 7   ADVVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIA 66

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

Query: 122 GLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEV--VENLVA 179
           GLPEV+LGLLPGAGGTQR PR +G + A+ +I+ G    A EAL  GL++ +   ++++A
Sbjct: 127 GLPEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILA 186

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

Query: 236 ADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPV 295
            DA+ AAI+ PF+EGL+ ER+ F++ + S Q     +AFFAERE  K        KPR +
Sbjct: 242 VDAVEAAIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETR-AAKPRTL 300

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

Query: 356 PAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSI 415
            A  M+  +G    + +  ADL+IEAVFE +AVK+ VF  +D   K GAVLA+NTSYL I
Sbjct: 361 KAALMSRWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDI 420

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

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

Query: 536 DRGIKS-------EIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKL 588
            R           +IAD LCE G FGQK+G+G+Y Y +GSR+  PDPEVE +I+   A+ 
Sbjct: 541 RRAATRNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARA 600

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

Query: 649 DSVGLKHIAERLSAYAKATNDPSL-EPAPLLARLAAEGKTFASLTQ 693
           D VGL  I   +  +AK   DP   +P+PLL  L   G  FASL Q
Sbjct: 661 DMVGLPKILADIREFAK--EDPLFWKPSPLLIELVERGADFASLNQ 704


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: 1187
Number of extensions: 55
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:

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. 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:

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:

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