Alignments for a candidate for ech in Mesorhizobium ciceri WSM1271

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Mesorhizobium ciceri WSM1271

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate YP_004140285.1 Mesci_1071 3-hydroxyacyl-CoA dehydrogenase NAD-binding protein

Query= BRENDA::P07896
         (722 letters)



>NCBI__GCF_000185905.1:YP_004140285.1
          Length = 688

 Score =  504 bits (1299), Expect = e-147
 Identities = 296/712 (41%), Positives = 426/712 (59%), Gaps = 36/712 (5%)

Query: 1   MAEYLRLPHS--LAMIRLCNPPVNAVSPTVIREVRNGLQKAGSDHTVKAIVICGANGNFC 58
           M++++++     +A++ + NPPVNA+S  V   +   L +   D +V AIVI  A   F 
Sbjct: 1   MSDFVKVSRDGDVAVVTIDNPPVNALSFHVREPLMQALVELRDDASVAAIVIACAGRTFV 60

Query: 59  AGADIHGFSAFTPGLALGSLVDEIQRYQKPVLAAIQGVALGGGLELALGCHYRIANAKAR 118
           AGADI  F        L ++V  ++   KP +AAI G ALGGGLELALGCH+R+A+A A+
Sbjct: 61  AGADITEFGKPMQQPELRAIVATLETIAKPTVAAIHGTALGGGLELALGCHFRVADAGAK 120

Query: 119 VGLPEVTLGILPGARGTQLLPRVVGVPVALDLITSGKYLSADEALRLGILDAVVKSDPVE 178
           +GLPEV LG+LPG  GT  LPR+VG   AL +I SG  + A EA   G++DAV + D   
Sbjct: 121 LGLPEVKLGLLPGGGGTVRLPRLVGAVKALKMIVSGAPIGATEAHAAGLVDAVFEGDLTT 180

Query: 179 EAIKFAQKIIDK--PIEPRRIFNKPVPSLPNMD-SVFAEAIAKVRKQYPGVLAPETCVRS 235
            A+ FA +I  K  P  P R  N+    L   D + F    A + ++  G+ AP  C +S
Sbjct: 181 HAVNFAGEIARKGGPFTPVRDRNE---GLKQADLAAFDVEAADLARKARGLEAPIACAQS 237

Query: 236 IQASVKHPYEVGIKEEEKLFMYLRASGQAKALQYAFFAEKSANKWSTPSGASWKTASAQP 295
           ++ +V  P++  +  E  LF+ L AS Q++A ++ FFAE+ A K         K    + 
Sbjct: 238 VRNAVTLPFDAALAAERALFVKLVASDQSRAQRHLFFAEREAAK------LPGKDIVKRR 291

Query: 296 VSSVGVLGLGTMGRGIAISFARVGISVVAVESDPKQLDAAKKIITFTLEKEASRAHQNGQ 355
           ++ VGV+G GTMG GIA++FA  G SV+ +E+  + L      I        +R   +  
Sbjct: 292 IARVGVIGAGTMGGGIAMAFANGGYSVILLETSHEALQRGLATIDRNYSVSVTRGSLSED 351

Query: 356 ASAKPKLRFSSSTK--ELSTVDLVVEAVFEDMNLKKKVFAELSALCKPGAFLCTNTSALN 413
           A  +   +F  ST   +L+  DL+VEAVFEDM +KK+VF +L A+ KPGA L TNTS L+
Sbjct: 352 AKRQRLAQFKGSTDYVDLADCDLIVEAVFEDMAVKKEVFGKLEAVAKPGAILATNTSYLD 411

Query: 414 VDDIASSTDRPQLVIGTHFFSPAHVMRLLEVIPSRYSSPTTIATVMSLSKKIGKIGVVVG 473
           +++IA ST RPQ V+G HFFSPA+VM+LLE++ +  ++P  +AT + L+++IGK+ VVVG
Sbjct: 412 INEIAGSTSRPQDVLGLHFFSPANVMKLLEIVRAEKTAPDALATSVDLARRIGKVAVVVG 471

Query: 474 NCYGFVGNRMLAPYYNQGFFLLEEGSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIR 533
            C+GFVGNRMLA   ++   LL EG+ P  +D V  +FG+ MGPF++ DLAGLD+GW+ R
Sbjct: 472 VCHGFVGNRMLAARGSESEALLLEGATPSQIDQVFTDFGWPMGPFQMGDLAGLDIGWRNR 531

Query: 534 KGQGLTGPSLPPGTPVRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDP 593
           K +G                  + + + D LCE GRFGQKTG+G+Y Y+    R   PDP
Sbjct: 532 KARG------------------QKAVIADTLCEQGRFGQKTGRGFYLYEAG-ARTPVPDP 572

Query: 594 WLSTFLSQYREVHHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDVIYLHGY 653
            +   +      + I  R IS EEI+ER LY LINE  +ILEEG+AAR   IDV++++GY
Sbjct: 573 EVEALIRDKAAENGIAPRAISAEEIVERTLYPLINEGAKILEEGIAARASDIDVVWVNGY 632

Query: 654 GWPRHKGGPMFYAASVGLPTVLEKLQKYYRQNPDIPQLEPSDYLRRLVAQGS 705
           G+P  KGGPMF+    G   ++E+L+ Y+ Q       +P+  L+R+   GS
Sbjct: 633 GFPIGKGGPMFWVGLEGPARIIERLE-YWHQRTGKDVFKPAPLLKRMAETGS 683


Lambda     K      H
   0.319    0.136    0.405 

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: 1062
Number of extensions: 49
Number of successful extensions: 7
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: 722
Length of database: 688
Length adjustment: 39
Effective length of query: 683
Effective length of database: 649
Effective search space:   443267
Effective search space used:   443267
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 24 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