GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__psRCH2:GFF442 Psest_0447 pyruvate dehydrogenase
           complex dihydrolipoamide acetyltransferase, long form
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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