GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Methylocapsa aurea KYG

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_036262823.1 DL86_RS14335 aldehyde dehydrogenase family protein

Query= curated2:Q87L22
         (485 letters)



>NCBI__GCF_000746085.1:WP_036262823.1
          Length = 506

 Score =  175 bits (444), Expect = 3e-48
 Identities = 146/466 (31%), Positives = 223/466 (47%), Gaps = 31/466 (6%)

Query: 3   HWIAGEWVQG-QGEEFVSLSPYNQEVIWRGNGATAEQVDQAVAAARAAFVEWKKRPFAER 61
           ++I G+WV   +G+ F ++SP +  VI     ++AE V+ A+ AA AA   W +   AER
Sbjct: 21  NFIGGKWVPAVKGQTFENISPIDGRVICTVARSSAEDVELALDAAHAARGAWGRTSPAER 80

Query: 62  EAIVLAFAEKVKENSEKIAEVIAKETGKPIWETRTEAAAMA----GKIAISIRAYHDRTG 117
              +L  A+++++  + +A V   + GKPI ET+     +A       A  +RA      
Sbjct: 81  SLALLRIADRIEQKLDMLAMVETIDNGKPIRETKAADLPLAVDHFRYFAGCLRAQEGGIS 140

Query: 118 EATREAAGNQIVLRHRPLGVMAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSEQTPWTG 177
           E   +         H PLGV+A   P+NFP  +    + PAL AGN V+ KP+EQTP + 
Sbjct: 141 EIDHDTVAYHF---HEPLGVVAQIIPWNFPLLMAVWKLAPALAAGNCVILKPAEQTPMS- 196

Query: 178 ELAMKLWEEAG--LPKGVINLVQG-AKETGIALADAKGIDGILFTGSANTGHILHRQFAG 234
              M L +  G  LP GV+N++ G   E G  LA  K I  + FTG   TG ++  Q+A 
Sbjct: 197 --VMVLVDMIGDLLPPGVLNVINGFGVEAGKPLAQNKRIAKVAFTGETTTGRLI-MQYAS 253

Query: 235 QPGKMLALEMGGNNPMVISDNYGDLDATVYTIIQSAF----ISAGQRCTCARRLYVPFGE 290
           +    + LE+GG +P +   +  D D   +      F    ++ G+ CTC  R  V   E
Sbjct: 254 ENIIPVTLELGGKSPNIFFADVADEDDDFFDKALEGFSMFALNQGEVCTCPSRALVQ--E 311

Query: 291 K-GDALITKLVEATKNIRMDQPFAEPAPFMGPQISVAAAKFIL-------DAQANLQSLG 342
           K  D  + + V   K I+   P  +PA  +G Q S    + IL          A + + G
Sbjct: 312 KIYDRFMERAVARVKKIKQGNPL-DPATMIGAQASNDQLEKILSYLDIGRQEGAKVLAGG 370

Query: 343 GESLIEAKAGEAAFVSPGIIDVTNIAELPDEEYFGPLLQVVRYEGLDKAVELANDTRFGL 402
           G + +  +     +V P I++  N   +  EE FGP+L V  ++  ++A+E+ANDT +GL
Sbjct: 371 GRADVGPELAGGFYVQPTILEGHNKMRIFQEEIFGPVLSVTSFKDDEEALEIANDTLYGL 430

Query: 403 SAGLVSTDDQEWEYFVDHIRAGIVNRNRQLTGASGDAPFGGPGASG 448
            AG+ + +      F   I AG V  N         A FGG   SG
Sbjct: 431 GAGVWTRNGTRAYRFGRAIEAGRVWTNCYHL-YPAHAAFGGYKQSG 475


Lambda     K      H
   0.316    0.134    0.397 

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: 533
Number of extensions: 27
Number of successful extensions: 5
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: 485
Length of database: 506
Length adjustment: 34
Effective length of query: 451
Effective length of database: 472
Effective search space:   212872
Effective search space used:   212872
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: 52 (24.6 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