GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Marinobacter guineae M3B

Align 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16) (characterized)
to candidate WP_099619082.1 CLH62_RS15420 acetyl-CoA C-acyltransferase

Query= reanno::MR1:200842
         (396 letters)



>NCBI__GCF_002744735.1:WP_099619082.1
          Length = 393

 Score =  510 bits (1314), Expect = e-149
 Identities = 254/390 (65%), Positives = 314/390 (80%)

Query: 7   NQEIVIVAAKRTPMGSFQGSLSGITSLSLAATAIKALLADTQVAPDKVDEVLMGCVLPAG 66
           +  +VI  + RTPMG   GSLS + S  L A AIKA +  + + P  V EV+MGCVLPAG
Sbjct: 3   DNSVVIAGSARTPMGGMMGSLSSVRSPDLGAAAIKAAIERSGLQPADVQEVIMGCVLPAG 62

Query: 67  LGQAPARQATLGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGGMESMSQ 126
           LGQAPARQA+  +G+P S G TT+NK+CGSGM+ V++AHD IKAG+  ++IAGGME+MSQ
Sbjct: 63  LGQAPARQASRASGIPDSSGCTTINKMCGSGMQAVIMAHDQIKAGTNNIMIAGGMENMSQ 122

Query: 127 APYLLDKARAGIRMGHGKVLDHMFLDGLEDAYTGGAMGTFAQKTADEFGITREQMDAFAL 186
           APYLL KARAG+RMGHG+V+D MFLDGLEDAY GG MG FAQ+TAD++ I+R+ MD FA+
Sbjct: 123 APYLLPKARAGMRMGHGQVMDSMFLDGLEDAYEGGLMGVFAQRTADKYDISRQAMDEFAI 182

Query: 187 SSLEKANAAINSGAFKTEIVPVTVSDRRGDVTIDTDEQPGNARPEKIPTLRPAFAKDGTI 246
            SL+K+ AAI +G F+ EIVPVTVS R GD  +DTDEQPGNA+PEKIP L+PAFAKDG++
Sbjct: 183 GSLQKSLAAIENGWFRDEIVPVTVSGRGGDTEVDTDEQPGNAKPEKIPHLKPAFAKDGSV 242

Query: 247 TAANSSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPALFTTAPVGAMAKLLS 306
           TAANSSSISDGA+AL+L + A A+  GLT  A I  H THA+ P+ FT AP+GA+ K+L 
Sbjct: 243 TAANSSSISDGASALVLASAAEADARGLTPQARIVAHATHARLPSEFTLAPIGAIEKVLK 302

Query: 307 NVGWSKDEVDLFEINEAFAMVTMLAVSELGLDMTKVNVNGGACALGHPIGCSGARLLVTL 366
             GWS D+VDLFEINEAFA+VT+ A++EL L   KVNV+GGACALGHPIG SG+R++VTL
Sbjct: 303 KAGWSVDDVDLFEINEAFAVVTLAAINELKLPAEKVNVHGGACALGHPIGSSGSRIIVTL 362

Query: 367 IHALKARGLKRGVASLCIGGGEATAMAIEV 396
           ++ALK RGLKRGVASLCIGGGE TA+AIE+
Sbjct: 363 MNALKQRGLKRGVASLCIGGGEGTAVAIEL 392


Lambda     K      H
   0.316    0.131    0.364 

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: 521
Number of extensions: 17
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: 396
Length of database: 393
Length adjustment: 31
Effective length of query: 365
Effective length of database: 362
Effective search space:   132130
Effective search space used:   132130
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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