GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Pseudomonas stutzeri RCH2

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate GFF442 Psest_0447 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form

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



>FitnessBrowser__psRCH2:GFF442
          Length = 667

 Score =  249 bits (636), Expect = 2e-70
 Identities = 160/432 (37%), Positives = 220/432 (50%), Gaps = 35/432 (8%)

Query: 6   IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65
           +++PD+G     A ++E  VK GD V  D  L  + +DKA++EIP+P  G V  L  +VG
Sbjct: 242 VRIPDIGSS-GSANVIEVMVKAGDSVEADQSLITLESDKASMEIPAPKAGIVESLSIKVG 300

Query: 66  DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQ---PE-KP 121
           D       ++ +   G A    P +  EA  +Q            +A AP +   PE K 
Sbjct: 301 DEARTGDLILTLRVQGTAPAKKPATKAEAAPQQ------------QAVAPNKQGVPEAKA 348

Query: 122 APKPAPAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISR-- 179
           A  PAPA         K  A PAVR+ ARE G++L  V  TGP GRI  ED+  ++    
Sbjct: 349 AATPAPAVSGPSKAGTKVHAGPAVRMLAREFGVELADVPATGPKGRILKEDVQAYVKNML 408

Query: 180 ---------------GAEPLPAQTGLVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITY 224
                          G  P+PA     R   VEEV M  L +  A  +  S   +PH+T 
Sbjct: 409 HKVKQAPAEGATGGAGIPPIPA-IDFSRFGEVEEVAMTRLMQVGAANLHRSWLNVPHVTQ 467

Query: 225 VEEVDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHR 284
            E  D+T LE  R       +    KLT+LP L++A    + E P  N++       + R
Sbjct: 468 FESADITELEAFRVAQKAIAEKAGVKLTVLPLLLKACAHLLKELPDFNSSLAPSGKALIR 527

Query: 285 HAAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITI 344
              VH+G A  TP GL VPV+R+ + + +   A E   LA+ ART   + D + G+  TI
Sbjct: 528 KKYVHVGFAVDTPDGLMVPVIRNVDQKSLLQLAGEAAELAEKARTKKLSPDAMQGACFTI 587

Query: 345 SSLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWD 404
           SSLG IGG   TP++N PEVAI+GV+K  ++PVWDG  F PR ++ LS S+DHRVI+G  
Sbjct: 588 SSLGHIGGTGFTPIVNAPEVAILGVSKATMQPVWDGKAFQPRLMLPLSLSYDHRVINGAA 647

Query: 405 AAVFVQRLKTLL 416
           AA F +RL  LL
Sbjct: 648 AARFTKRLSELL 659



 Score = 60.1 bits (144), Expect = 2e-13
 Identities = 36/101 (35%), Positives = 56/101 (55%), Gaps = 4/101 (3%)

Query: 6   IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65
           IK+PD+G  + +A ++E  VKPGD +  +  L  + +DKA++EIPSP  G V  +  +VG
Sbjct: 127 IKVPDIGS-LGKASVIEIAVKPGDTIAAEQALITLESDKASMEIPSPAAGVVESISVKVG 185

Query: 66  DTVAVKAPLVRIETAG---EAGEAAPDSIPEALAEQVLDEP 103
           D V     ++ ++ A     A   AP S   +  +Q L EP
Sbjct: 186 DEVGTGDLILVLKGAAPSKPAASKAPASQAASAPKQKLSEP 226



 Score = 59.3 bits (142), Expect = 3e-13
 Identities = 37/111 (33%), Positives = 57/111 (51%), Gaps = 5/111 (4%)

Query: 6   IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65
           I++PD+G G  E E++E  VK GD +  D  +  + +DKA++EIP+P  G V  L  ++G
Sbjct: 5   IRVPDIGSG--EGEVIELFVKVGDRIEADQSILTLESDKASMEIPAPKAGVVKSLKVKLG 62

Query: 66  DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPP 116
           D +     L+ +E+      AAP    +A AE         +   EA  PP
Sbjct: 63  DRLKEGDELLELESEDGQDSAAPS---QAAAEPAGAASGGPTDETEAPTPP 110


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: 650
Number of extensions: 21
Number of successful extensions: 5
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: 667
Length adjustment: 35
Effective length of query: 391
Effective length of database: 632
Effective search space:   247112
Effective search space used:   247112
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