GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucO in Rhodococcus qingshengii djl-6-2

Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate WP_003942060.1 C1M55_RS09025 iron-containing alcohol dehydrogenase

Query= metacyc::STM4044-MONOMER
         (382 letters)



>NCBI__GCF_002893965.1:WP_003942060.1
          Length = 401

 Score =  251 bits (641), Expect = 3e-71
 Identities = 143/370 (38%), Positives = 208/370 (56%), Gaps = 2/370 (0%)

Query: 14  GAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMSYHLFDEVFPNPTE 73
           G G++ +  +        +  +VTD  L+  G +  L   L E  ++  ++  + PNP +
Sbjct: 33  GIGSLVEAAHATLRFGGFRPFLVTDPGLIDAGWVSELEDHLTEQGLTATVWSGLTPNPKD 92

Query: 74  ELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYSGVGKVKNAGVPLV 133
             +  GF  YQ  ECD IIA GGGS ID AK V +L AN G    Y GV +      PLV
Sbjct: 93  FEIAAGFEVYQEGECDVIIALGGGSVIDAAKGVAVLAANGGNILDYEGVDQATKPIPPLV 152

Query: 134 AINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVMLEIPASVTAATGMD 193
            + TT+GT A+++   ++ D+ R  K  II   ++PD+ V D  ++  +P  + AATG+D
Sbjct: 153 MVPTTSGTGADVSQFCIVTDTTRGTKITIIGRALVPDVTVIDPRLLTTMPEWLNAATGLD 212

Query: 194 ALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEAREQMAFGQYLAGMAF 253
           ALTH +EA+VS+  +PLTD +AL A+ L+   L   + D   +EAR  MA     AG+AF
Sbjct: 213 ALTHGIEAFVSLAHNPLTDHHALRAVGLVTENLVHTIQDPMEMEARSVMAQASLEAGLAF 272

Query: 254 NSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFARIAQAMGV-ETRG 312
            +A LG  HA++HQ G   +LPHGV N ILLP V  FN     A F  IA A+ + E RG
Sbjct: 273 TNAILGAAHAMSHQVGGMLDLPHGVINGILLPHVIRFNSTTDAAPFVAIAAALSLPEQRG 332

Query: 313 MSDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDIEGWLDKALADPCAPCNPRTASRD 372
             +EAA   A + +  L++ VG+P+G  +LGV +ED+      AL D C   NPR A+++
Sbjct: 333 TPEEAALAVA-DRVERLAREVGVPKGLGELGVREEDLSRLASFALLDACMSTNPREATQE 391

Query: 373 EVRGLYLEAL 382
           ++  L+  AL
Sbjct: 392 QMVALFRGAL 401


Lambda     K      H
   0.317    0.133    0.384 

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: 452
Number of extensions: 23
Number of successful extensions: 1
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: 382
Length of database: 401
Length adjustment: 31
Effective length of query: 351
Effective length of database: 370
Effective search space:   129870
Effective search space used:   129870
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: 50 (23.9 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:

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