GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Dinoroseobacter shibae DFL-12

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate 3608649 Dshi_2042 aminotransferase class-III (RefSeq)

Query= reanno::pseudo5_N2C3_1:AO356_13150
         (454 letters)



>FitnessBrowser__Dino:3608649
          Length = 460

 Score =  242 bits (618), Expect = 2e-68
 Identities = 150/436 (34%), Positives = 230/436 (52%), Gaps = 28/436 (6%)

Query: 18  HHLAPFSDFKQLKEKGPRIITHAKGVYLWDSEGNKILDGMAG-LWCVAVGYGREELADAA 76
           HHL    + K  +   PRII   KG+ +WD+ G + LD ++G LW V VGYGRE +A+A 
Sbjct: 23  HHLI---NHKPFETTDPRIIVEGKGMRVWDALGKEHLDAVSGGLWTVNVGYGRERIANAV 79

Query: 77  SQQMRELPYYNLFFQTAHPPVLELSKAIADIAPEGMNHVFFTGSGSEGNDTMLRMVRHYW 136
             Q+ ++ +++    T   P    S+ + D  P GM+ V++  SGSE N+   +MVR   
Sbjct: 80  RDQLMQMCFFSNSLGTI--PGAIFSEMLIDKMP-GMSRVYYASSGSEANEKAFKMVRQIA 136

Query: 137 AIKGQPNKKVIISRKNGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIAQPYWFGEGGDM 196
                  K  I+ R+  YHGST+A  S GG      Q     P  V +  P+        
Sbjct: 137 HKVHGGRKTKILYRERDYHGSTLATMSAGGQWERKAQYGPFAPDFVEV--PHCLEYRAQW 194

Query: 197 SPEEFGVWAANQLEEKILEIGVDNVGAFIAEPIQGAGGVIVPPDSYWPRMKEILAKYDIL 256
             E +G  AA+ +EE IL  G D VGA   EP+   GGVI PP+ YWPR++EI  KYD+L
Sbjct: 195 EGENYGERAADAIEEVILREGPDTVGALCLEPVTAGGGVITPPEGYWPRVQEICRKYDVL 254

Query: 257 FVADEVICGFGRTGEWFGTDHYGLKPHMMTIAKGLTSGYIPMGGLIVRDDVVAVL-NEGG 315
              DEV+CG GRTG+WFG  HYG++P  +T+AKG+ SGY  +  ++  + V  +  +E G
Sbjct: 255 LHIDEVVCGLGRTGKWFGYQHYGIEPDFVTMAKGVASGYAAISCMVTTERVFEMFKSEPG 314

Query: 316 D----FNHGFTYSGHPVAAAVALENIRILRDEKII---ERVHSETAPYLQKRLRELNDHP 368
                F    T+ G     A A+EN++I+ +E ++   +R+H +    L   + +   H 
Sbjct: 315 APLDYFRDISTFGGCTAGPAAAIENMKIIEEEDLLGNTDRMHDQLMGNLAGLMEK---HR 371

Query: 369 LVGEVRGVGLLGAIELVQDKATRKRYEGKGVGMICRQFCFDNGLIMRAV-------GDTM 421
           ++G++RG GL    ELV D+ T++      V  +    C   G+I+ A         +T+
Sbjct: 372 VIGDIRGKGLFCGAELVADRTTKEPAPEALVQAVVAD-CMAQGVIIGATNRSLPGYNNTL 430

Query: 422 IIAPPLVISKAEIDEL 437
             +P L+ +  +ID++
Sbjct: 431 CFSPALIATADDIDQI 446


Lambda     K      H
   0.320    0.139    0.431 

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: 593
Number of extensions: 34
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: 454
Length of database: 460
Length adjustment: 33
Effective length of query: 421
Effective length of database: 427
Effective search space:   179767
Effective search space used:   179767
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 (21.8 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