Alignments for a candidate for pimF in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for pimF in Cupriavidus basilensis 4G11

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate RR42_RS10265 RR42_RS10265 3-hydroxyacyl-CoA dehydrogenase

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



>FitnessBrowser__Cup4G11:RR42_RS10265
          Length = 692

 Score =  640 bits (1652), Expect = 0.0
 Identities = 337/685 (49%), Positives = 465/685 (67%), Gaps = 14/685 (2%)

Query: 13  VAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEFGKPP 72
           VA++++ +PPVN L   VR GI++ ++ A AD  V+AIVL  AG+ F  GAD+ EF  P 
Sbjct: 11  VAVISIANPPVNGLGYDVRVGIIDGIDRAAADDNVRAIVLTGAGKAFSGGADMREFNSPE 70

Query: 73  --QPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVKLGL 130
             + P LN V+ A+ENS K  +AA+H  A+GGGLE+AL CH+RVAV +A++ L EV +GL
Sbjct: 71  AWREPGLNTVLVAIENSIKLVVAAVHSVAMGGGLELALACHYRVAVPKARIALSEVTMGL 130

Query: 131 LPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE-NLVAGAVAFAKKVL 189
           LPGAGGTQRLPR +G E A  MIV G+ I +      GL + +VE ++V  AVAFA++V 
Sbjct: 131 LPGAGGTQRLPRLIGLEAATNMIVHGTSIPSEALADTGLFDRLVEGDVVTAAVAFAQEVA 190

Query: 190 AEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGAAIDLPFEE 249
           A   P  R+RD   +    +   ++   AVAA  K    L+AP  C DAI A+  LPF+E
Sbjct: 191 ARPGPHPRVRDLTIRHPTPEGYLAVARPAVAARYKN---LQAPLRCLDAIEASFKLPFDE 247

Query: 250 GLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTMGGG 309
           GL  ER  F++L+    SK+ R+AFF+ER AAK+  VPD    R V++VA++GAG MG G
Sbjct: 248 GLALERRLFLELMNGPVSKSLRHAFFSERAAAKLADVPDSVPERAVNKVAVVGAGLMGSG 307

Query: 310 IAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGLVGL 369
           IAM+F +AGIPV L++  +E +++G   +++N+EA+  +G L  +    RMAL+   V L
Sbjct: 308 IAMNFLSAGIPVVLLDISDEVVQKGAAAIRRNYEASLKKGKLRAEVVEARMALLQPTVDL 367

Query: 370 ENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQDVL 429
             V   DL+IEA++E M VK  +F A+D  A+PGA+LA+NTS L +D IAA T+RPQDV+
Sbjct: 368 GRVAACDLVIEAIYEDMDVKLRMFRALDEIARPGAILATNTSMLDVDRIAAETRRPQDVV 427

Query: 430 GMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLAARS 489
           G+HFFSPANVM+L E+VRGAKTAPD L TA+ +A++I KVPVV GVCDGF+GNRMLA  +
Sbjct: 428 GLHFFSPANVMRLLEVVRGAKTAPDVLQTAMRLARRIGKVPVVSGVCDGFIGNRMLAKYT 487

Query: 490 KQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRGIKS------EI 543
           +++ +LL +GA P+QVD  + +FG+ MGPF M DLAG DIGW  RK    +       E+
Sbjct: 488 RRAGELLEQGAFPEQVDRAIEEFGLAMGPFRMADLAGNDIGWAIRKRHYAEDPSQPRFEL 547

Query: 544 ADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDEEILER 603
            D LCEAG FGQKTG G+Y YE G R  +P      ++     + G+  R  + +EI+ER
Sbjct: 548 GDRLCEAGHFGQKTGTGWYDYEAGQRKALPSARTRAMLEAYWKERGVVPRRFSGQEIVER 607

Query: 604 MVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAERLSAY 663
           ++Y ++NEGA +L+E IAAR SDID V+L+GYG+P +RGGPM YAD+VG+ ++   L A 
Sbjct: 608 LIYALVNEGAAVLDEGIAARASDIDAVYLHGYGFPAWRGGPMFYADTVGVTNVRRTLRAL 667

Query: 664 AKATNDPSLEPAPLLARLAAEGKTF 688
             +  DPS +PA L+ +LA +G+TF
Sbjct: 668 --SAKDPSWKPAALIEQLADKGRTF 690


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: 1119
Number of extensions: 61
Number of successful extensions: 6
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: 692
Length adjustment: 39
Effective length of query: 660
Effective length of database: 653
Effective search space:   430980
Effective search space used:   430980
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