GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF in Pedobacter sp. GW460-11-11-14-LB5

Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase

Query= SwissProt::P42236
         (488 letters)



>FitnessBrowser__Pedo557:CA265_RS14635
          Length = 501

 Score =  288 bits (738), Expect = 2e-82
 Identities = 182/462 (39%), Positives = 254/462 (54%), Gaps = 14/462 (3%)

Query: 10  YLNFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRKLTG 69
           Y N+I G++V    G      +P D   +     +ST ED+E AV AA+EA   W K + 
Sbjct: 14  YDNYIGGKFVAPVKGAYFDNISPID-GKVFTKAAHSTKEDLELAVDAAHEAFKTWSKTSS 72

Query: 70  AERGQYLYKTADIMEQRLEEIAACATREMGKTLPEA-KGETARGIAILRYYAGEGMRKTG 128
            ER   L K A  ME  LE +AA  T + GK + E    +   G+   RY+AG    + G
Sbjct: 73  TERSIILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADLPLGVDHFRYFAGVIRAEEG 132

Query: 129 DVIPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAVT 188
             +   D++ +      P+GVV  I PWNFP+ + IWK+APAL  GN VV+KPA  T V+
Sbjct: 133 S-LSELDQNTVSLIVHEPIGVVAQIIPWNFPLLMGIWKLAPALAAGNCVVLKPAESTPVS 191

Query: 189 CAKIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAALAR 248
              ++    +  LP GV+N+V G GS +G+ L  +  V+   FTGS   G+++ Q A   
Sbjct: 192 IMVLMELIGDL-LPPGVVNVVNGFGSELGRALVTNPKVSKAAFTGSTPTGRLVMQYATEN 250

Query: 249 GAKYQLEMGGKNP------VIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSGIY 302
                LE+GGK+P      V+  DDA L+ A E  +  A    G+ CT  SR+++Q  IY
Sbjct: 251 IIPVTLELGGKSPNIFFSSVMAEDDAFLDKAVEGAVMFALNQ-GEICTCPSRLLIQEDIY 309

Query: 303 ERFKEKLLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEKLE 362
           E+F  K+++RTK I IG  L   V MG  ASK Q +   +YI+ GK+EGA +L GGE  E
Sbjct: 310 EKFIAKVIERTKAIKIGSPLDRTVMMGAQASKIQFEKIAAYIKLGKEEGAEVLTGGEINE 369

Query: 363 -NGKYQNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSAS 421
             G+   GYY++P IF    ++M I QEEIFGPV+A+    ++EEA+ IAND  +GL A 
Sbjct: 370 LPGELGGGYYIKPTIFKG-HNKMRIFQEEIFGPVLAVTTFKTVEEAIEIANDTLYGLGAG 428

Query: 422 IFTENIGRMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQS 463
           ++T +   +      I AG V +N   A     APFGG KQS
Sbjct: 429 VWTRDAHELYQVPRAIQAGRVWVNQYHA-YPAGAPFGGYKQS 469


Lambda     K      H
   0.315    0.132    0.374 

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: 573
Number of extensions: 25
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: 488
Length of database: 501
Length adjustment: 34
Effective length of query: 454
Effective length of database: 467
Effective search space:   212018
Effective search space used:   212018
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 (21.5 bits)
S2: 52 (24.6 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:

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