GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Herbaspirillum seropedicae SmR1

Align Gluconate 2-dehydrogenase cytochrome c (characterized, see rationale)
to candidate HSERO_RS18760 HSERO_RS18760 cytochrome C

Query= uniprot:A4PIB1
         (441 letters)



>FitnessBrowser__HerbieS:HSERO_RS18760
          Length = 499

 Score =  263 bits (672), Expect = 9e-75
 Identities = 162/429 (37%), Positives = 226/429 (52%), Gaps = 44/429 (10%)

Query: 27  AYAADADLIKRGAYVAVLGDCEACHTAHDGKSLAGGLALQSPLGAIYSTNITPDRDTGIG 86
           A + +A LI+RG Y+A+  DC ACHTA  GK +AGGLA+ SP+G I +TNITP +  GIG
Sbjct: 45  AISPEAALIERGHYLAIASDCIACHTAPRGKPMAGGLAIASPVGEIIATNITPSKTHGIG 104

Query: 87  TWSYEDFARLMRRGIRKDGSSVYPAMPYPSYSKMTDEDLQALYAYLTQGVAPVSLKNRAP 146
            ++ E FA  +RRG+R DG+++YPAMPY +Y+ ++D D+QALYAY  +GVAPV +  R  
Sbjct: 105 NYTEEQFAAALRRGVRADGANLYPAMPYTAYAALSDADVQALYAYFMKGVAPVDVATRPT 164

Query: 147 DIPWLLSARWPLAIWRLLF-APSPAPPLPSAPHDDTSDALVERGRYLVEGPGHCGSCHTP 205
           D+P+ ++ RW +  W  LF    P PP P         A   RGRYL EGP HC +CHTP
Sbjct: 165 DLPFPMNLRWSMKAWNALFLKEQPLPPQPQ------RSAQWLRGRYLAEGPAHCSTCHTP 218

Query: 206 RNFVLAEKVQTAADGPKYLSGGFIVDNWVAPSLRSDDAGGLVGWTPEDIVAFLKTGR-NR 264
           R +++ EK       P     G  V  W AP++ S  + G+  W+ +D+VA+L+TGR   
Sbjct: 219 RGWLMQEK-------PDLQLAGAQVGPWYAPNITSHPSAGIGSWSQDDLVAYLRTGRLEG 271

Query: 265 HGATFGAMNGVITHSTSLTDDHDLAAIAAFLK-----TLGPPPGVSVQAFHYDDTVSRQL 319
                G+M   ITHS S   + DL AIA ++K       G   G   +        +   
Sbjct: 272 RAQAAGSMAEAITHSFSRLTEEDLRAIAVYIKDRPAIATGDAQGSGSRFDQGKAGNALAQ 331

Query: 320 FAGKMPS-------EGARIYVDRCAACHRTDGHG-YPGVFPPLAGNPVLQGPDATSAAHI 371
           F G+  S        GARI+   CA+CH  +G G   G +P L  N    G +A +    
Sbjct: 332 FRGRTLSAESPEEIRGARIFSASCASCHGYNGQGSRDGYYPSLFRNSATAGVNANNLIAT 391

Query: 372 IL--------SGGR--LPGVAAAPSSLVMGSYRDVLDNQQIADLVTFLGQSWGNHGAAMT 421
           IL         GG   +P     P++L      + L N  +A L  +L + +G   A + 
Sbjct: 392 ILYGVDRETEQGGHVFMPPFGDQPNAL------NKLSNADVAALSNYLLKYYGKPAATVK 445

Query: 422 ASQVAKIRQ 430
           A  V  IRQ
Sbjct: 446 AEDVEVIRQ 454



 Score = 38.9 bits (89), Expect = 4e-07
 Identities = 42/138 (30%), Positives = 60/138 (43%), Gaps = 23/138 (16%)

Query: 166 APSPAPPL-PSAPHDDTSDALVERGRYLVEGPGHCGSCHT-PRNFVLAEKVQTAADGPKY 223
           AP+PAP + P A       AL+ERG YL      C +CHT PR   +A  +  A+     
Sbjct: 39  APAPAPAISPEA-------ALIERGHYLAIA-SDCIACHTAPRGKPMAGGLAIASP---- 86

Query: 224 LSGGFIVDNWVAPSLRSDDAGGLVGWTPEDIVAFLKTGRNRHGAT-FGAMNGVITHSTSL 282
                 V   +A ++      G+  +T E   A L+ G    GA  + AM    T   +L
Sbjct: 87  ------VGEIIATNITPSKTHGIGNYTEEQFAAALRRGVRADGANLYPAM--PYTAYAAL 138

Query: 283 TDDHDLAAIAAFLKTLGP 300
           +D    A  A F+K + P
Sbjct: 139 SDADVQALYAYFMKGVAP 156


Lambda     K      H
   0.318    0.135    0.420 

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: 630
Number of extensions: 30
Number of successful extensions: 8
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: 441
Length of database: 499
Length adjustment: 33
Effective length of query: 408
Effective length of database: 466
Effective search space:   190128
Effective search space used:   190128
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 (21.7 bits)
S2: 51 (24.3 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