GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Pseudomonas putida KT2440

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate PP_0214 PP_0214 4-aminobutyrate aminotransferase

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



>FitnessBrowser__Putida:PP_0214
          Length = 425

 Score =  217 bits (553), Expect = 5e-61
 Identities = 142/397 (35%), Positives = 206/397 (51%), Gaps = 33/397 (8%)

Query: 34  SRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHVS-NVFTNEPALRLA-- 90
           S V D  GRELIDFAGGIAV   GH HP +VAA+ EQ  K+ H    V   EP + L   
Sbjct: 34  STVIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTKVSHTCFQVLAYEPYVELCEK 93

Query: 91  -HKLVDATFAERVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSFHGRTLFTV 149
            +KLV   F ++     +G+EA E A K+AR        T +  ++A    +HGRT+ T+
Sbjct: 94  INKLVPGDFDKKTLLVTTGSEAVENAVKIARAA------TGRAGVIAFTGGYHGRTMMTL 147

Query: 150 NVGGQS-KYSDGFGPKITGITHVPY----------NDLAALKAAVSDKT-----CAVVLE 193
            + G+   YS G G    GI    +          + +A+++    +        A++LE
Sbjct: 148 GLTGKVVPYSAGMGLMPGGIFRALFPSELHGISVDDAIASVERIFKNDAEPRDIAAIILE 207

Query: 194 PIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGVTPDILTS 253
           P+QGEGG LPA    ++  R LCD H  LL+ DEVQTG GR+G  FA +  GV PD+ T 
Sbjct: 208 PVQGEGGFLPAPKELMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQMGVAPDLTTF 267

Query: 254 AKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLNGVNA 313
           AKS+ GGFP+A +    +    +  G  G TY G+P+ACA A AVI+V    ++L+   A
Sbjct: 268 AKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVIEVFEEEKLLDRSKA 327

Query: 314 KHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAW-----KGKAKDIFNAAEREGLMI 368
             ++    L +I +KY +  +VRGLG ++   + +             +   A  +GL++
Sbjct: 328 VGERLTAGLREIQKKYPIIGDVRGLGSMIAVEVFEKGTHTPNAAAVGQVVAKAREKGLIL 387

Query: 369 LQAGP--DVIRFAPSLVVEDADIDAGLDRFERAAAKL 403
           L  G   +V+R    L  EDA +D GL   E   A++
Sbjct: 388 LSCGTYGNVLRILVPLTAEDALLDKGLAIIEECFAEI 424


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: 433
Number of extensions: 22
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: 406
Length of database: 425
Length adjustment: 31
Effective length of query: 375
Effective length of database: 394
Effective search space:   147750
Effective search space used:   147750
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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