GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Shewanella halifaxensis HAW-EB4

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate WP_012275606.1 SHAL_RS02430 dihydrolipoyllysine-residue acetyltransferase

Query= reanno::Smeli:SMc03203
         (426 letters)



>NCBI__GCF_000019185.1:WP_012275606.1
          Length = 555

 Score =  237 bits (605), Expect = 6e-67
 Identities = 154/432 (35%), Positives = 228/432 (52%), Gaps = 30/432 (6%)

Query: 6   IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65
           + +PD+G+  ++ +++E  V  GD +  D  L  + TDKAT+E+P+P  G V  L   VG
Sbjct: 125 VSVPDIGDA-SDVDVIEVLVAVGDKIDADTGLITLETDKATMEVPAPSAGIVKELKVAVG 183

Query: 66  DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125
           D V++ + ++ +E + +A  AAP     A +      P  V+    A  PP P  P+   
Sbjct: 184 DKVSMGSLVLMLEVS-DAAPAAPVVAAPATSTPAPVAPAPVAQAASANKPPVPHHPSAGS 242

Query: 126 APAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFI-------- 177
            P        +    ASPAVR  ARE G DL  V GTG  GRI  ED+  FI        
Sbjct: 243 QPK-------TGAVHASPAVRRLAREFGADLTLVKGTGRKGRILKEDVQAFIKYELSRPK 295

Query: 178 -------SRGAEPLPA----QTGLVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITYVE 226
                  + GA  L      +    +   VEEV +  +++     +  +   IPH+T  +
Sbjct: 296 ASAATAVAGGAGGLSVIAAPKVDFAKFGEVEEVPLSRIQKISGPNLHRNWVTIPHVTQFD 355

Query: 227 EVDMTALEDLRATMNR--DRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHR 284
           E D+T LE  R   N    +K    K+T L F+M+A+ KT+AE P  N++       + +
Sbjct: 356 EADITELEAFRKDQNAVAAKKKADYKITPLVFMMKAVAKTLAEFPVFNSSLSADGESLIQ 415

Query: 285 HAAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITI 344
               HIG+A  TP GL VPVVR  + +GI + + EL  ++  AR G     ++ GS  TI
Sbjct: 416 KKYFHIGVAVDTPNGLMVPVVRDVDKKGIVELSRELTEISVKARDGKLKAADMQGSCFTI 475

Query: 345 SSLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWD 404
           SSLG IGG A TP++N+P+VAI+GV+K  ++P W+G +F P+ ++ LS S+DHRVIDG  
Sbjct: 476 SSLGGIGGTAFTPIVNYPDVAILGVSKSEIKPKWNGKEFEPKLMLPLSLSYDHRVIDGAM 535

Query: 405 AAVFVQRLKTLL 416
           AA F   L ++L
Sbjct: 536 AARFSVTLSSIL 547



 Score = 54.7 bits (130), Expect = 7e-12
 Identities = 37/121 (30%), Positives = 58/121 (47%), Gaps = 10/121 (8%)

Query: 6   IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65
           + +PD+G    E +++E     GD +  +  +  V +DKAT++IP+P  G +  L   VG
Sbjct: 7   VLIPDIGGD--EVQVIEICAAVGDTLAAEESIITVESDKATMDIPAPFAGVLSELKVAVG 64

Query: 66  DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125
           DTV+    +  +  AG       +S P A        P AV + + A+AP   E PA   
Sbjct: 65  DTVSEGTLIAMMSAAGAQAPTEVESTPAA--------PDAVQAPVAAQAPAPEEAPAASV 116

Query: 126 A 126
           A
Sbjct: 117 A 117


Lambda     K      H
   0.317    0.133    0.384 

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: 547
Number of extensions: 28
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 426
Length of database: 555
Length adjustment: 34
Effective length of query: 392
Effective length of database: 521
Effective search space:   204232
Effective search space used:   204232
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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