GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acdH in Burkholderia phytofirmans PsJN

Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate BPHYT_RS28040 BPHYT_RS28040 acyl-CoA dehydrogenase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2983
         (375 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS28040 BPHYT_RS28040 acyl-CoA
           dehydrogenase
          Length = 377

 Score =  476 bits (1226), Expect = e-139
 Identities = 233/371 (62%), Positives = 293/371 (78%)

Query: 5   DDQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTGY 64
           D+Q+ IRD ARDFA E+L P A +WDRE + P E + +M  LGF GM+VP +WGG  T Y
Sbjct: 7   DEQRMIRDAARDFATEQLAPHAGQWDREAQLPAEVVRQMGELGFLGMIVPAEWGGSYTDY 66

Query: 65  LAYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGAFALT 124
           +AYA+ALEEIAAG  AC+T+MSVHNSVGC PILN+GT+ QK+R+L+ LA+G  +GAF LT
Sbjct: 67  VAYALALEEIAAGCAACATLMSVHNSVGCGPILNFGTEAQKDRYLQDLATGRRIGAFCLT 126

Query: 125 EPQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIV 184
           EPQAGS+A+ L+TRA L    ++LNG KQF+T+G  A + IVFAVTDP  GKRG++AFIV
Sbjct: 127 EPQAGSEANNLRTRAVLRDGKWILNGSKQFVTNGSRADLAIVFAVTDPDRGKRGLTAFIV 186

Query: 185 PTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGGRVGI 244
           PTD+PG+ V + E KLG  ASDTC I  +D  VP AN LGE GEG RIAL+NLEGGR+GI
Sbjct: 187 PTDTPGFNVGKPEHKLGIRASDTCPISLDDCAVPEANLLGEPGEGLRIALSNLEGGRIGI 246

Query: 245 ASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALR 304
           A+Q+VG+ARAAF+AAR YA ER  FGK + EHQ +A  LADMAT++  AR +VH+AA LR
Sbjct: 247 AAQAVGIARAAFDAARLYANERIQFGKALKEHQTIANMLADMATRLNAARLLVHHAARLR 306

Query: 305 DSGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIYEGTS 364
            +GKP L EAS AKLFASE+AE++CS+A+Q  GGYGYL D+ VER YRD R+ QIYEGTS
Sbjct: 307 TAGKPCLSEASQAKLFASELAEEICSNAIQIHGGYGYLEDYAVERHYRDARITQIYEGTS 366

Query: 365 DIQRMVISRNL 375
           ++QRM+I+R++
Sbjct: 367 EVQRMLIARHV 377


Lambda     K      H
   0.320    0.135    0.394 

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: 419
Number of extensions: 11
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: 375
Length of database: 377
Length adjustment: 30
Effective length of query: 345
Effective length of database: 347
Effective search space:   119715
Effective search space used:   119715
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 (21.8 bits)
S2: 50 (23.9 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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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