GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcmA in Chryseobacterium arthrosphaerae CC-VM-7

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_065399519.1 BBI00_RS15060 methylmalonyl-CoA mutase family protein

Query= BRENDA::Q8F222
         (1125 letters)



>NCBI__GCF_001684965.1:WP_065399519.1
          Length = 1115

 Score = 1468 bits (3800), Expect = 0.0
 Identities = 735/1125 (65%), Positives = 902/1125 (80%), Gaps = 10/1125 (0%)

Query: 1    METQIYTPKHKVRFITAASLFDGHDASINIMRRILQSSGVEVIHLGHNRSVREIVECAIQ 60
            METQ YTP +KVR +TAASLFDGHDA+INIMRR++Q +G EVIHLGH++S  E+V  AIQ
Sbjct: 1    METQKYTPTNKVRIVTAASLFDGHDAAINIMRRVIQGTGCEVIHLGHDKSAEEVVNTAIQ 60

Query: 61   EDAQGIAITSYQGGHVEYFKYMIDLLKEKGAGHIKVFGGGGGTILPSEIKELESYGVTRI 120
            EDA  IA+TSYQGGH EYFKY+ DLL+EK +  IK+FGGGGG ILP EIK+L SYG+ RI
Sbjct: 61   EDANAIALTSYQGGHNEYFKYIYDLLREKNSPQIKIFGGGGGVILPEEIKDLMSYGIDRI 120

Query: 121  YSPDDGRELGLQGMINDLIRRSDFIPPITFNGTLHSSLKDKNPLAIAQMITLVENTFERE 180
            YSPDDGRELGLQGMI+DL+ RSDF             +  +NP +IAQ+I+ VEN  E  
Sbjct: 121  YSPDDGRELGLQGMIDDLVHRSDFATGKDVTAKDLDDISFENPSSIAQIISAVENFSE-- 178

Query: 181  DLEKSTLNEKLNFPPGTKSVPVLGITGTGGAGKSSLTDELVRRFLIDFPNKTIAILSVDP 240
              EK  L + ++      ++P++GITGTGGAGKSSLTDELVRRFL    +K IAI+S+DP
Sbjct: 179  --EKPELVKAIDEESKHLNIPIIGITGTGGAGKSSLTDELVRRFLRSNTDKKIAIISIDP 236

Query: 241  SKRKTGGALLGDRIRMNSISHDRVYMRSFATREANIALNKNVKRSIEVLKSAGFDLIIVE 300
            SK+KTGGALLGDRIRMN+I+  RVYMRS ATRE N++++  +  ++ VLK A  D+II+E
Sbjct: 237  SKKKTGGALLGDRIRMNAINDPRVYMRSMATRENNVSVSPFIHSALNVLKLAHPDVIILE 296

Query: 301  TAGIGQSDSEITEVADVALYVMTPEYGAATQLEKIDMIDYADLIAINKFDKRGALDALRD 360
            T+GIGQS SE+++ ADV++YVMTPEYGA+TQLEKIDM+DYADL+A+NK DKRGALDAL+ 
Sbjct: 297  TSGIGQSGSEVSDFADVSMYVMTPEYGASTQLEKIDMLDYADLVALNKSDKRGALDALQA 356

Query: 361  VKKQFQRSRQLFDQNIDLMPVFGTIASQFNDPGTNLLYGNVIRFLSNKLNLDWSSSYEKE 420
            V+KQFQR+  L++  +D MPV+ T ASQFND GT  LY  ++  ++ K   + S     E
Sbjct: 357  VRKQFQRNHLLWESPLDDMPVYATKASQFNDHGTTELYNRLVSKVNEKFP-ELSLKTFVE 415

Query: 421  EGASEKIFIIPPDRVRYLAEIREECGRYDQFTKNESDKARKLFQLSGAIEVLKSSGQDIS 480
            +  +E++ IIPP RVRYL+EI E   +YD   + +++ ARK++ + G   ++ +      
Sbjct: 416  QEVTEEVTIIPPKRVRYLSEIVENNKQYDANIEKQAELARKMYHIEGVKAIISNE----- 470

Query: 481  ILKLEYSKIENSLSLETKKILSSWEEKLKNYQGENFTYKVRDKEIKVSNTTVSLSNLKIP 540
            +L+ EY K E  L  E    L +W++  K +  E ++Y VR KEIKV  +T SLS+L+IP
Sbjct: 471  VLEAEYQKAEKELQQENIDFLKTWDDTKKAFHAEFYSYFVRGKEIKVETSTESLSHLRIP 530

Query: 541  KVAVPKFKDWGEIVRWSFQENFPGEFPFTSGVFPFKRTGEDPTRMFAGEGGPERTNARFH 600
            K+A+PK+ DWG++++W  QEN PG FP+T+G++PFKRTGEDPTRMFAGEGGPERTN RFH
Sbjct: 531  KIALPKYNDWGDLIKWKGQENLPGSFPYTAGIYPFKRTGEDPTRMFAGEGGPERTNRRFH 590

Query: 601  YVSLGMPAQRLSTAFDSVTLYGEDPGERPDIYGKIGNSGVSIATLDDAKKLYSGFDLCNP 660
            YVS  MPA+RLSTAFDSVTLYG+DP   PDIYGKIGN+GVSIATLDDAKKLYSGFDL N 
Sbjct: 591  YVSAEMPAKRLSTAFDSVTLYGQDPALPPDIYGKIGNAGVSIATLDDAKKLYSGFDLVNA 650

Query: 661  TTSVSMTINGPAPMVLAFFMNTAIDQACEKHILASGIEKSVRQKIESIYKEKKFPIPKYN 720
             TSVSMTINGPAPM+LAFFMN AIDQ  EK+I  +G+E  V  K++  + +K    PKYN
Sbjct: 651  LTSVSMTINGPAPMLLAFFMNAAIDQNVEKYIKENGLEAKVEAKLKEKFDDKGLERPKYN 710

Query: 721  TQIPEGNDGLGLMLLGVTGDEVLEKEVYEKIKQETLKLVRGTVQADILKEDQAQNTCIFS 780
             ++P  N+GLGL LLG+TGDEV+  +VY +IK +T+  VRGTVQADILKEDQAQNTCIFS
Sbjct: 711  GELPPSNNGLGLQLLGLTGDEVIPADVYAEIKAKTIATVRGTVQADILKEDQAQNTCIFS 770

Query: 781  TEFALKMMGDIQEFFIKNQVRNFYSVSISGYHIAEAGANPITQVAFTLANGLTYVEYFLS 840
            TEFAL++MGD+QE+FIK +VRNFYSVSISGYHIAEAGANP++Q+AFTLANG TYVEY+LS
Sbjct: 771  TEFALRLMGDVQEYFIKEKVRNFYSVSISGYHIAEAGANPVSQLAFTLANGFTYVEYYLS 830

Query: 841  RGMKIDDFAPNLSFFFSNGIDPEYAVIGRVARRIWAKAMKYKYGANDRSAMLKYHIQTSG 900
            RGM I+DFAPNLSFFFSNGIDPEY+VIGRVARRIWAKAMK KYGA++RS MLKYHIQTSG
Sbjct: 831  RGMDINDFAPNLSFFFSNGIDPEYSVIGRVARRIWAKAMKLKYGADERSQMLKYHIQTSG 890

Query: 901  RSLHAQEIAFNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTEESVRRAMAIQLIINRE 960
            RSLHAQEI FNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTE+SVRRAMAIQLIIN+E
Sbjct: 891  RSLHAQEIDFNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTEQSVRRAMAIQLIINKE 950

Query: 961  LGLSKNENPSQGSFIIEELTDLVEQAILEEFHKISERGGVLGAMEMMYQRNKIQEESLYY 1020
            LGL+KNENP QGSFIIEELTDLVE+A+  EF +I+ERGGVLGAME MYQR+KIQEES++Y
Sbjct: 951  LGLAKNENPLQGSFIIEELTDLVEEAVYTEFDRITERGGVLGAMETMYQRSKIQEESMHY 1010

Query: 1021 ESLKHNGEFPVIGVNTFLSKEGSPTIVPQEVIRSTDEEKQAQISALREFHKRNEKDIENR 1080
            E LKH GE+P+IGVNTFL K+GSPT++P EVIRST+EEKQAQI  L  F K NE   E  
Sbjct: 1011 EWLKHTGEYPIIGVNTFLGKDGSPTVLPGEVIRSTEEEKQAQIEFLHNFQKANESKSEEA 1070

Query: 1081 LRKLKSVSLSNGNIFQELMETSKKVSLGQMTHALYEVGGQYRRSM 1125
            LR L+  +++  N+F+ +M+  K  SLGQ+T+AL+EVGG+YRR+M
Sbjct: 1071 LRTLQHAAINQQNLFEVMMDAVKYCSLGQITNALFEVGGKYRRNM 1115


Lambda     K      H
   0.317    0.135    0.379 

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: 3179
Number of extensions: 130
Number of successful extensions: 5
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: 1125
Length of database: 1115
Length adjustment: 46
Effective length of query: 1079
Effective length of database: 1069
Effective search space:  1153451
Effective search space used:  1153451
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: 58 (26.9 bits)

This GapMind analysis is from Sep 24 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