GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Jannaschia aquimarina GSW-M26

Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_043917574.1 jaqu_RS03630 betaine-aldehyde dehydrogenase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_495
         (480 letters)



>NCBI__GCF_000877395.1:WP_043917574.1
          Length = 485

 Score =  324 bits (830), Expect = 5e-93
 Identities = 185/470 (39%), Positives = 274/470 (58%), Gaps = 6/470 (1%)

Query: 14  FIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKERA 73
           F+DGAWV+  +G  + V  PATG+++  V     A   RA+ +A  A   W A    ER 
Sbjct: 12  FVDGAWVEDQDGPALDVVYPATGKVVARVHGATDAVLDRALASAAGAQTEWAATDPAERG 71

Query: 74  TKLRRWYELIIENQDDLARLMTLEQGKPLAEAK-GEIVYAASFIEWFAEEAKRIYGDVIP 132
             LRR  +LI     DL+ L TL+ GKPL E    +    A  +E+F   A  I G+ + 
Sbjct: 72  RILRRAADLIRARNRDLSELETLDTGKPLQETLVADAASGADALEYFGALAADIRGETM- 130

Query: 133 GHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAFAL 192
                     I++P+GV A I  WN+P  +   KA PALAAG  MV KP+  TP  A  +
Sbjct: 131 -RFGADWAYTIRRPLGVCAGIGAWNYPTQIACWKAAPALAAGNAMVFKPSEATPLGALRI 189

Query: 193 AELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAKDIKKV 252
           AE+   AG+PAG+F+VV G  G +G+ LT++  V K+S TGS   GR++    A  +K V
Sbjct: 190 AEILHEAGLPAGLFNVVQGD-GRVGATLTTDRRVAKVSLTGSVPTGREVAGAAAGAMKHV 248

Query: 253 SLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAEKLKVA 312
           ++ELGG +P ++F+DADL  AV GAI   + ++GQ C    R+++Q G+ DAF  +L   
Sbjct: 249 TMELGGKSPLLIFEDADLGDAVSGAINGNFYSSGQVCSNGTRVFVQRGLRDAFVSRLTER 308

Query: 313 VAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPM--EGNFFEPTI 370
           +A + IG+ L+  T  GP+  E  +  V +HI  A ++GATV AGG  +  EG + EPTI
Sbjct: 309 LAGVVIGDPLDEATNYGPMTTEAQMRIVLDHIGRARAEGATVGAGGTRIDREGYWIEPTI 368

Query: 371 LTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRVFRVAEA 430
           LT++ ++ A  +EE FGP+  +  F+DE + IA +N T FGLA+  + RDL R  RVA A
Sbjct: 369 LTDLTDDMACVREEIFGPVLSVLTFEDEDEAIARANATGFGLAAGIFTRDLTRAHRVAAA 428

Query: 431 LEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGI 480
           ++ G + +N   ++    PFGG K SG+GRE ++  ++ Y E++ + +G+
Sbjct: 429 MQAGTIWINQYNLTPAGMPFGGSKMSGIGRENARAALDHYTEVQTIYVGM 478


Lambda     K      H
   0.317    0.135    0.390 

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: 589
Number of extensions: 23
Number of successful extensions: 4
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: 480
Length of database: 485
Length adjustment: 34
Effective length of query: 446
Effective length of database: 451
Effective search space:   201146
Effective search space used:   201146
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: 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