GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdA in Shewanella loihica PV-4

Align 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial; Branched-chain alpha-keto acid dehydrogenase E1 component alpha chain; BCKDE1A; BCKDH E1-alpha; EC 1.2.4.4 (characterized)
to candidate 5209454 Shew_1925 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (RefSeq)

Query= SwissProt::P12694
         (445 letters)



>FitnessBrowser__PV4:5209454
          Length = 392

 Score =  368 bits (945), Expect = e-106
 Identities = 183/383 (47%), Positives = 250/383 (65%), Gaps = 2/383 (0%)

Query: 57  ASAEFIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMD 116
           ++ E + ++ F+  + +S IPI +++   G     +  P + ++   K+Y +      +D
Sbjct: 6   SNTETVHRVSFLDKDSLS-IPILKILQADGTTFENAVLPVIDQDLAAKIYDTCVFTRVLD 64

Query: 117 RILYESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMA 176
             +  +QRQGRISFYMT  GEE   VGS AALD  D++  QYRE   + YR +  E FM 
Sbjct: 65  ERMLAAQRQGRISFYMTCTGEEAAVVGSVAALDQDDVILAQYREHAAIRYRGFTTEQFMN 124

Query: 177 QCYGNISDLGKGRQMPVHYGCKERHFVTISSPLATQIPQAVGAAYAAKRANANRVVICYF 236
           Q + N  DLGKGRQMP+HYGC+  ++ TISSPLATQIPQA G  Y+ K      V ICYF
Sbjct: 125 QMFSNEKDLGKGRQMPIHYGCEALNYQTISSPLATQIPQATGVGYSLKMQGKRNVAICYF 184

Query: 237 GEGAASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSI 296
           GEGAASEGD HAG N AA L  P+IFFCRNNGYAISTPT+EQ+ G+GIA+RG GYG+ +I
Sbjct: 185 GEGAASEGDFHAGLNMAAVLNSPVIFFCRNNGYAISTPTNEQFAGNGIASRGVGYGMHTI 244

Query: 297 RVDGNDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDK 356
           RVDGND+ AV  AT++AR  A+  N+P LIEAMTYR+G HS+SDD S YRS DE   W +
Sbjct: 245 RVDGNDMLAVMAATQQARAYALEHNKPVLIEAMTYRLGAHSSSDDPSGYRSKDEEAKWQQ 304

Query: 357 QDHPISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERKPKPNPNLLFSDVYQEM 416
            D P+ R + +L+++GW  E  + A  ++ R +V+ A + AE+ P P  + +  DV  E 
Sbjct: 305 HD-PVKRFKLWLINKGWLAESDDAALYEKYREEVLAAVKVAEKLPAPKIDEIIEDVLDEP 363

Query: 417 PAQLRKQQESLARHLQTYGEHYP 439
             +L++Q   L +H++ Y + YP
Sbjct: 364 TPRLKQQLTELKQHIKKYPDSYP 386


Lambda     K      H
   0.320    0.135    0.405 

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: 453
Number of extensions: 13
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: 445
Length of database: 392
Length adjustment: 32
Effective length of query: 413
Effective length of database: 360
Effective search space:   148680
Effective search space used:   148680
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: 50 (23.9 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