GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Herbaspirillum seropedicae SmR1

Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate HSERO_RS19695 HSERO_RS19695 aldehyde dehydrogenase

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



>FitnessBrowser__HerbieS:HSERO_RS19695
          Length = 480

 Score =  373 bits (958), Expect = e-108
 Identities = 191/467 (40%), Positives = 287/467 (61%), Gaps = 2/467 (0%)

Query: 12  QAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKE 71
           Q +IDG +   +  +  +V +PATG++LG +P    A+   AI+AA +A   WR ++  E
Sbjct: 6   QLYIDGRFHGVEGRRYQEVRDPATGDVLGRLPWAERADIEEAIQAAHRAFQQWRQVSPLE 65

Query: 72  RATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRIYGDVI 131
           R+  LRR   L  E    +A  +T++ GKPLA+A  EI+ AA  ++W AEE +R+YG V+
Sbjct: 66  RSDILRRAAALARERAQAMAPAITMDNGKPLADAVAEIINAAEHLDWHAEEGRRLYGRVV 125

Query: 132 PGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAFA 191
               P+ R +V+++P+GV AAI+PWNFP     +K   A+AAGCT+VLK  S++P +   
Sbjct: 126 GARHPEVRQLVVREPVGVCAAISPWNFPFGQAMKKVAAAMAAGCTVVLKGPSESPAAIVL 185

Query: 192 LAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAKDIKK 251
           +A+L   AG+PAGVF++VSG + +I   L  +P+VR +SFTGS  +G +L ++ A  +K+
Sbjct: 186 MAQLFHDAGVPAGVFNIVSGVSSEISQHLIESPLVRNISFTGSVPVGSKLAAQAALHMKR 245

Query: 252 VSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAEKLKV 311
           +S+ELGG+AP +VFDDA+++ A       K RN GQ CV  +R Y+Q G+Y  F      
Sbjct: 246 MSMELGGHAPVLVFDDAEVEPAARLLARLKTRNAGQVCVSPSRFYVQKGIYARFVTAFAE 305

Query: 312 AVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPM--EGNFFEPT 369
           A+ ++K+G G E G   GPLI  +    VQ  I DAL++G+ ++ GG  +   G+F+ PT
Sbjct: 306 ALLQIKVGPGHEPGVQMGPLIHGRRFEAVQGLIDDALAQGSELVTGGARLGQRGHFYAPT 365

Query: 370 ILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRVFRVAE 429
           ++T VP +A V +EE FGP+A +  F    + IAM+N    GLASY + + L    RV+ 
Sbjct: 366 LITGVPPSARVMQEEPFGPIAAVTPFSQAEEAIAMANALPLGLASYVFTQSLDTAHRVSR 425

Query: 430 ALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYL 476
            L+ GMV +N   +++   PFGGI  SG G EG   G E +L  K +
Sbjct: 426 DLQAGMVNINHSGMAHPELPFGGIGESGFGSEGGVEGFESFLVTKMI 472


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: 562
Number of extensions: 25
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: 480
Length of database: 480
Length adjustment: 34
Effective length of query: 446
Effective length of database: 446
Effective search space:   198916
Effective search space used:   198916
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: 51 (24.3 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