GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Herbaspirillum seropedicae SmR1

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate HSERO_RS23240 HSERO_RS23240 omega amino acid--pyruvate aminotransferase

Query= reanno::pseudo1_N1B4:Pf1N1B4_3440
         (406 letters)



>FitnessBrowser__HerbieS:HSERO_RS23240
          Length = 442

 Score =  152 bits (383), Expect = 2e-41
 Identities = 121/409 (29%), Positives = 180/409 (44%), Gaps = 42/409 (10%)

Query: 20  NYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHVSN 79
           N+  A  + V   G    D +G  ++D   G+    LGHAHP +V+A+ +    L +  +
Sbjct: 24  NFKAAPRMLVSAEGMHYRDDAGNTILDGTAGLWCVPLGHAHPKIVSAVQKSVATLDYAPS 83

Query: 80  VFTNEP-ALRLAHKLVDATFAE--RVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVA 136
                P A  LA +L   T      VF+  SG+EA + A K+A      +    +  ++ 
Sbjct: 84  FQLGHPSAFELAERLKAYTGNRFGNVFYTGSGSEAVDTALKIALAYHRAKGNATRTRLIG 143

Query: 137 ALNSFHGRTLFTVNVGGQSKYSDGFGPKIT-GITHVPYNDLAALKAAV------------ 183
               +HG     ++VGG       F   +  G+ H+P+       A              
Sbjct: 144 RERGYHGVGFGGMSVGGIGGNRKTFSTALLPGVDHLPHTHNLEKNAFTKGEPEYGAHLAD 203

Query: 184 ----------SDKTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMG 233
                     +    AV++EP+ G  GVL     YL+  RE+C  H  LL+FDEV TG G
Sbjct: 204 ELERLVTLHDASNIAAVIVEPVAGSTGVLIPPKGYLKRLREICTKHGILLIFDEVITGFG 263

Query: 234 RSGKLFAYQHYGVTPDILTSAKSLGGG-FPIAAMLTTEDLAKHLVVGT------HGTTYG 286
           R G  FA  ++ V PDI T+AK L  G  P+ A+    ++    + G       HG TY 
Sbjct: 264 RLGTPFASDYFDVEPDIFTTAKGLTNGVVPMGAVFVKPEIHDAFMNGPDGIELFHGYTYS 323

Query: 287 GNPLACAVAEAVIDVINTPEVLNGVNAKHDKFKTRLEQIGEKYGL--FTEVRGLGLLLGC 344
           G+PLACA   A ++V  T  VL    A  D F+   E      GL    +VR +GL+ G 
Sbjct: 324 GHPLACAAGLASLEVFQTEGVLENAQAVADYFQ---EAAHALRGLPHVIDVRTIGLIAGI 380

Query: 345 VLSD---AWKGKAKDIFNAAEREGLMILQAGPDVIRFAPSLVVEDADID 390
            L+        +A D F  A  +G++I   G D+I  +P L++    ID
Sbjct: 381 ELASIPGRVGARAYDAFVRAFNDGILIRVTG-DIIALSPPLIINKQQID 428


Lambda     K      H
   0.320    0.136    0.400 

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: 443
Number of extensions: 24
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: 406
Length of database: 442
Length adjustment: 32
Effective length of query: 374
Effective length of database: 410
Effective search space:   153340
Effective search space used:   153340
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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