Alignments for a candidate for pimF in Xenophilus azovorans DSM 13620

GapMind for catabolism of small carbon sources

Alignments for a candidate for pimF in Xenophilus azovorans DSM 13620

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate WP_038214718.1 Q392_RS25280 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

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



>NCBI__GCF_000745855.1:WP_038214718.1
          Length = 709

 Score =  647 bits (1668), Expect = 0.0
 Identities = 345/701 (49%), Positives = 466/701 (66%), Gaps = 14/701 (1%)

Query: 4   VVTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGA 63
           V+  A   +V  +T+D+PPVNA+S+AVRRG+ E V AA AD  V+AI++V  G  F+AGA
Sbjct: 11  VIRSARHGEVLCITIDNPPVNAISSAVRRGLKEAVEAADADAGVKAILIVGEGANFVAGA 70

Query: 64  DITEFGKPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGL 123
           DI EFG+ PQPP+L +V   +E+  KP +AAI G ALGGGLE+AL  H+RVA+ +A+LGL
Sbjct: 71  DIREFGQAPQPPSLPEVCNRIEDCAKPVVAAIRGAALGGGLEIALAAHWRVALADARLGL 130

Query: 124 PEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVV--ENLVAGA 181
           PEV+LGL+PGAGGT R PR  G + A+ +++ G  + A EAL  GLV+ +   E+  A  
Sbjct: 131 PEVQLGLMPGAGGTVRAPRLAGAQAALDLMLSGRHVKAKEALSLGLVDRIADGEDAQAAG 190

Query: 182 VAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGA 241
           +A+A ++LA+   +RR RD    LA   A ++    A A   KK+RGL +P    +A+  
Sbjct: 191 LAYANELLAQGAGVRRTRDAQG-LADRAAAQAAIDAAKADTAKKSRGLFSPMKIVEAVQT 249

Query: 242 AIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAII 301
           A+D PFEE +K ERE F+  + S Q     +AFFAERE AKV       +PR ++ V I+
Sbjct: 250 ALDKPFEEAVKLEREAFLACIDSPQRAGLIHAFFAEREVAKVPEAK-AAQPRVLNSVGIV 308

Query: 302 GAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMA 361
           G GTMG GIA+S  +AG+PV ++E  +  ++RG   ++K ++    +G + P+A A  MA
Sbjct: 309 GGGTMGAGIAVSALDAGLPVVMVERDQPSIERGRANVEKVYDGLIRKGRMTPEAKAAVMA 368

Query: 362 LITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAAT 421
             TG      + D DL+IEAVFE + VKK VF  +D   K GAVLA+NTSYL ID IAA+
Sbjct: 369 RYTGATDYAALADVDLVIEAVFEDIEVKKAVFKELDRVCKAGAVLATNTSYLDIDAIAAS 428

Query: 422 TKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVG 481
           T RPQDV+G+HFFSPAN+MKL EIV  AK + D + TA ++AKK+ KVPV  GVCDGF+G
Sbjct: 429 TSRPQDVIGLHFFSPANIMKLLEIVVPAKVSADVVSTAFALAKKMKKVPVRAGVCDGFIG 488

Query: 482 NRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRGIKS 541
           NR+LA   + ++ ++ +GA P ++D  V  FG PMGPF + DLAG DIGW +RK R    
Sbjct: 489 NRILAVYKQAADYIMEDGASPYEIDEAVRGFGYPMGPFQVTDLAGGDIGWATRKRRAATR 548

Query: 542 -------EIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRD 594
                  E+AD +CE G FGQKTG+G+Y Y +G+R   PDPEV  +++    K G+  R 
Sbjct: 549 DPKARYVEVADRVCERGWFGQKTGRGFYLYPEGARVGQPDPEVLAIVDAERQKKGITPRQ 608

Query: 595 ITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLK 654
            T EEI+ R +  M+NEGA+++EE IA RP D+DV +LYGYG+P +RGGPM YAD VGL 
Sbjct: 609 FTAEEIMRRYMAAMVNEGAKVVEEGIALRPLDVDVTFLYGYGFPRHRGGPMKYADMVGLP 668

Query: 655 HIAERLSAYAKATNDPSL-EPAPLLARLAAEGKTFASLTQP 694
            I E + A+AK   DP   +PAPLL +L AEG+ FASL QP
Sbjct: 669 KILEDIRAFAK--EDPLFWKPAPLLEKLVAEGRDFASLNQP 707


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: 1242
Number of extensions: 71
Number of successful extensions: 5
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: 709
Length adjustment: 39
Effective length of query: 660
Effective length of database: 670
Effective search space:   442200
Effective search space used:   442200
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 Apr 09 2024. 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 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