GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Desulfoscipio geothermicus DSM 3669

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_207545101.1 BM299_RS02525 4-aminobutyrate--2-oxoglutarate transaminase

Query= reanno::pseudo6_N2E2:Pf6N2E2_4013
         (425 letters)



>NCBI__GCF_900115975.1:WP_207545101.1
          Length = 434

 Score =  407 bits (1045), Expect = e-118
 Identities = 203/438 (46%), Positives = 286/438 (65%), Gaps = 19/438 (4%)

Query: 1   MSKTNADLMARRTAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60
           M+KTNA+L+AR+   + RG+     +F E A+ AT+ DVEG+E+IDF GGI  LN GH  
Sbjct: 1   MAKTNAELVARKHQLIARGISNSTEVFVEKAQGATIVDVEGKEYIDFYGGIGTLNAGHCP 60

Query: 61  PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120
             ++ A+  Q  KL HTCF V  YEPY++L EK+    PG+F K+ + V +G+E VENAV
Sbjct: 61  APVVEAIKNQAEKLLHTCFMVTMYEPYLDLAEKLIELTPGNFDKRVMFVNSGAECVENAV 120

Query: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIF------------ 168
           KIAR+   R G+I+F  A+HGRT+MT+ LT KV PY  G G     ++            
Sbjct: 121 KIARSYAKRTGIISFECAFHGRTLMTMSLTSKVKPYKFGFGPFAPEVYKIPSAYCYRCTY 180

Query: 169 RALYPN-ELHGVSIDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLR 227
           R+ YP   LH       +   +R+F  +  P +IAA+IIEPVQGEGGF V P EF+  LR
Sbjct: 181 RSTYPECGLH------CLEQFDRMFAAEVPPENIAAMIIEPVQGEGGFIVPPPEFLPGLR 234

Query: 228 ALCDQHGILLIADEVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYM 287
            +CD+HGI+LIADEVQTG GRTG  FA E  G+  DL T AKSIA G PL+ V GKA+ M
Sbjct: 235 KICDKHGIILIADEVQTGFGRTGKMFACEHFGLEPDLMTMAKSIAAGMPLSAVVGKADIM 294

Query: 288 DAIAPGGLGGTYAGSPIACAAALAVMEVFEEEHLLDRCKAVGERLVAGLKAIQKKYPVIG 347
           +A  PG +GGTY+G+P++CAA LA ++  ++++L++R   +G++    + A+Q+KYP+IG
Sbjct: 295 NAPNPGEIGGTYSGNPVSCAAGLATIDFMQQQNLVERANVIGDKTKQRMLAMQEKYPIIG 354

Query: 348 DVRALGAMIAVELFENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTAP 407
           DVR LGAM A+EL ++ ++ +P     A V+    D G+I++  G + NV+R L+PL   
Sbjct: 355 DVRGLGAMNAMELVKDRNTKEPAKEETAAVIKHCVDNGVIVIGAGIFSNVVRTLIPLVIT 414

Query: 408 DEQLDKGLAILEECFSEL 425
           DEQL+KGL +LE+  + +
Sbjct: 415 DEQLEKGLDVLEQAVASV 432


Lambda     K      H
   0.320    0.137    0.395 

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: 533
Number of extensions: 23
Number of successful extensions: 2
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: 425
Length of database: 434
Length adjustment: 32
Effective length of query: 393
Effective length of database: 402
Effective search space:   157986
Effective search space used:   157986
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 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