GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Herbaspirillum seropedicae SmR1

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate HSERO_RS11260 HSERO_RS11260 aldehyde dehydrogenase

Query= BRENDA::Q72IB9
         (516 letters)



>FitnessBrowser__HerbieS:HSERO_RS11260
          Length = 477

 Score =  241 bits (615), Expect = 4e-68
 Identities = 169/484 (34%), Positives = 247/484 (51%), Gaps = 22/484 (4%)

Query: 41  YIGGEWV--DTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFK-TWKDWPQED 97
           +I   WV   + E +  L+PS   +     A+    + + A+ AA  A++  W      +
Sbjct: 5   FIANRWVAPTSGESIPVLDPS-DGQPFDAIARGNATDIDQAVRAARLAYEGAWGRLSAAE 63

Query: 98  RSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAV 157
           RSRLL+K A  ++  + EL      + GK   +A AD A  + + E+YA AA +      
Sbjct: 64  RSRLLMKLAYKLQDHQEELAQLEGRDCGKPMKQARADAAAIVRYFEFYAGAADKLHG--- 120

Query: 158 EVVPYP-GEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVG 216
           + +PY  G    +   P G    I PWN+P+ IF   + G +A GNT + KPAEDA +  
Sbjct: 121 DTIPYQAGYTVLTLREPHGVTGHIVPWNYPMQIFGRCVGGALAAGNTCVVKPAEDACLSI 180

Query: 217 AKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLA 276
            +V E+  E GFP G +N + G G E G  LV+HP    I+FTGS  VG  +  AA    
Sbjct: 181 LRVAELAAEVGFPEGALNIVTGYGHEAGDLLVKHPDVNHISFTGSPNVGKLVVRAAAEHH 240

Query: 277 PGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYE 336
              T      +E GGK   IV E AD +     VV +     GQ CSA SRL++ +GAYE
Sbjct: 241 TPVT------LELGGKSPQIVFEDADMEAMLPVVVNAIVQNAGQTCSAGSRLLVQRGAYE 294

Query: 337 PVLERVLKRAERLSVGPAEENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGKRLEG- 394
            VLER+     +L VG ++ + D GP++   Q+ +V  ++   + +G  L   GK   G 
Sbjct: 295 QVLERLSGLFSQLQVGSSQMDLDCGPLIRKTQQERVAGFLSDAQRDGIALAAQGKIAAGV 354

Query: 395 --EGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSR 452
              G++ AP +  +VPP+ R+AQEE+FGPVL+ +  +D A A+ +AN T YGL   V++R
Sbjct: 355 PTGGFYQAPALLRDVPPRHRLAQEEVFGPVLAAMPFEDEAHAIALANGTDYGLVASVWTR 414

Query: 453 KREHLEWARREFHVGNLYFNRKITGALVGVQ-PFGGFKLSGTNAKTGALDYLRLFLEMKA 511
                    R    G ++ N    GA  GV+ PFGG K SG   + G  + L  F  +K 
Sbjct: 415 DGGRQMRLARAIRSGQVFINN--YGAGGGVELPFGGVKASGHGREKG-FEALYGFTVLKT 471

Query: 512 VAER 515
           +A R
Sbjct: 472 IAIR 475


Lambda     K      H
   0.319    0.137    0.403 

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: 566
Number of extensions: 30
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: 516
Length of database: 477
Length adjustment: 34
Effective length of query: 482
Effective length of database: 443
Effective search space:   213526
Effective search space used:   213526
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 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