GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Shewanella sp. ANA-3

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate 7023193 Shewana3_0427 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase (RefSeq)

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



>FitnessBrowser__ANA3:7023193
          Length = 668

 Score =  241 bits (616), Expect = 4e-68
 Identities = 152/434 (35%), Positives = 232/434 (53%), Gaps = 35/434 (8%)

Query: 6   IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65
           I++PD+G+  +  +++E  V  GD +  D  L  + TDKAT+E+P+P  GK+L L  +VG
Sbjct: 239 IQVPDIGDA-SNVDVIEVLVSVGDMITADQGLITLETDKATMEVPAPFAGKLLSLTVKVG 297

Query: 66  DTVAVKAPLVRIETAGEAGEAAPDSI-PEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPK 124
           D V+  + +  IET       AP +  P  +A++    PVA +       PP P  P+  
Sbjct: 298 DKVSQGSVIATIETVTAGAAPAPQAAAPAPVAQEAAPAPVAAAP----SRPPVPHHPSAG 353

Query: 125 PAPAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFI------- 177
                  AP  +    ASPAVR  ARE G+DL QV G+G  GRI  ED+  ++       
Sbjct: 354 -------APVATGVVHASPAVRRLAREFGVDLTQVTGSGRKGRIMKEDVQAYVKYELSRP 406

Query: 178 -SRGAEPLPAQTG------------LVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITY 224
            +  A  + A  G              +   VEE+ +  +++     +  +   IPH+T 
Sbjct: 407 KATAATSVAAGNGGGLQVIAAPKVDFSKFGEVEEIPLSRIQKISGPNLHRNWVTIPHVTQ 466

Query: 225 VEEVDMTALEDLRATMN--RDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVI 282
            +E D+T +E+ R   N    +K    K+T L F+M+A+ KT+ + P  N++       +
Sbjct: 467 FDEADITEMEEFRKQQNDAAAKKKADYKITPLVFMMKAVAKTLQQFPVFNSSLSSDGESL 526

Query: 283 HRHAAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTI 342
            +    HIG+A  TP GL VPVVR  + +GI + + EL  ++  AR G     ++ GS  
Sbjct: 527 IQKKYYHIGVAVDTPNGLVVPVVRDVDKKGIIELSRELADISIRARDGKLKSADMQGSCF 586

Query: 343 TISSLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDG 402
           TISSLG IGG A TP++N+P+VAI+GV+K  ++P W+G +F P+ ++ LS S+DHRVIDG
Sbjct: 587 TISSLGGIGGTAFTPIVNYPDVAILGVSKSEIKPKWNGKEFEPKLMLPLSLSYDHRVIDG 646

Query: 403 WDAAVFVQRLKTLL 416
             AA F   L  +L
Sbjct: 647 AMAARFSVTLSGIL 660



 Score = 57.4 bits (137), Expect = 1e-12
 Identities = 43/130 (33%), Positives = 65/130 (50%), Gaps = 11/130 (8%)

Query: 6   IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65
           + +PD+G G  +  ++E  V  GD +  D  L  + TDKAT+++PSP  G V  +   VG
Sbjct: 126 VTVPDIG-GDTDVSVIEVLVAAGDKIEVDAGLITLETDKATMDVPSPFAGVVKEVKVAVG 184

Query: 66  DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125
           D V+  + ++ +E  G A  AA    P+A A      PVA ++   A A   P   AP  
Sbjct: 185 DKVSQGSLVIMLEVGGAAPAAA---APQASA----SAPVAQAAPAAAVA---PVAAAPVV 234

Query: 126 APAPREAPDL 135
           A    + PD+
Sbjct: 235 AVKEIQVPDI 244



 Score = 49.7 bits (117), Expect = 3e-10
 Identities = 40/124 (32%), Positives = 59/124 (47%), Gaps = 23/124 (18%)

Query: 8   MPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVGDT 67
           +PD+G    E +++E     GD +  +  +  V +DKAT++IP+P  G +  L   VGD 
Sbjct: 9   VPDIGGD--EVQVIEICASVGDTLAAEESILTVESDKATMDIPAPFAGVLAELKVAVGDK 66

Query: 68  VAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAP-PQPEKPAP-KP 125
           V+    +  ++ AG A   A               PVA     +A AP P P  PAP + 
Sbjct: 67  VSEGTLIAMMQAAGTANVQA--------------APVA-----QAAAPAPAPAAPAPVQA 107

Query: 126 APAP 129
           APAP
Sbjct: 108 APAP 111


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: 686
Number of extensions: 33
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 426
Length of database: 668
Length adjustment: 35
Effective length of query: 391
Effective length of database: 633
Effective search space:   247503
Effective search space used:   247503
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 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