GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Stutzerimonas stutzeri A1501

Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_011913066.1 PST_RS09725 acyl-CoA dehydrogenase family protein

Query= metacyc::MONOMER-11693
         (386 letters)



>NCBI__GCF_000013785.1:WP_011913066.1
          Length = 383

 Score =  265 bits (678), Expect = 1e-75
 Identities = 157/382 (41%), Positives = 227/382 (59%), Gaps = 7/382 (1%)

Query: 2   DHRLTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGG 61
           D  L+ +   +R    +FA   +AP    + +       +V +MG +GL G+  PEE+GG
Sbjct: 3   DLELSEDQRMIRDMARDFARREIAPHAQAWEKAGWIDDALVAQMGELGLLGMVVPEEWGG 62

Query: 62  MGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILG 121
              DY+A  +A+EE++  D +    +    S+G  P+  +G+ AQK EWL  L SG  +G
Sbjct: 63  SYIDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLAELASGRAIG 122

Query: 122 AFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKPD 181
            F LTEP  GS+A   RT A L +   +WV+NG+K F +N+      L  V AVT   PD
Sbjct: 123 CFALTEPQAGSEAHNLRTRAELVDG--QWVLNGSKQFCSNAKR--AKLAIVFAVTD--PD 176

Query: 182 -GKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQF 240
            GK  +S+ +VP+ T GF V     K+G  ASDT  +S +D R+P ANLLGE+G+G A  
Sbjct: 177 LGKKGLSAFLVPTDTAGFAVERSEHKMGIRASDTCAVSLSDCRIPQANLLGERGKGLAIA 236

Query: 241 LRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMA 300
           L  L+ GRI I A A G+A+   + ++ YA ER  FG+ I  +Q+I   +ADM+ + + A
Sbjct: 237 LSNLEGGRIGIGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAA 296

Query: 301 RVGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRD 360
           R+    AA    AG P   EA+ AKL++S +A     +A QIHGGYG++ +YPV R +RD
Sbjct: 297 RLLILHAARLKSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYYRD 356

Query: 361 SKILEIGEGTSEVQRMLIAREL 382
           ++I +I EG+SE+QR+LIAREL
Sbjct: 357 ARITQIYEGSSEIQRLLIAREL 378


Lambda     K      H
   0.318    0.136    0.402 

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: 379
Number of extensions: 16
Number of successful extensions: 3
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: 386
Length of database: 383
Length adjustment: 30
Effective length of query: 356
Effective length of database: 353
Effective search space:   125668
Effective search space used:   125668
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 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:

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