GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iatA in Herbaspirillum seropedicae SmR1

Align Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate HSERO_RS05320 HSERO_RS05320 ribonucleotide-diphosphate reductase subunit alpha

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__HerbieS:HSERO_RS05320
          Length = 502

 Score =  369 bits (948), Expect = e-106
 Identities = 217/512 (42%), Positives = 312/512 (60%), Gaps = 17/512 (3%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           +L ++ + K+F  V  L  VDL V  GEVHALLGENGAGKSTL+KIL      DAG +  
Sbjct: 1   MLQLTGIKKNFGPVTVLRGVDLEVRAGEVHALLGENGAGKSTLMKILCGIVRPDAGEIRI 60

Query: 63  AGQV--LDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPR-RLGLVDWSRLRA 119
            GQ    D   A +     G+  ++QEF+L P L   +NM+L RE R R G +  + +R 
Sbjct: 61  DGQPCRFDSYRAAIAG---GVGVVFQEFSLIPYLDAVDNMFLARELRSRWGWLQRAAMRR 117

Query: 120 DAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRL 179
            AQ ++  LG+ +  D PV  L+VA+QQ VEIAKA+ L+AR++++DEPTA L+  EV+ L
Sbjct: 118 RAQEIIGQLGVAIPLDVPVCKLSVAQQQFVEIAKALALDARILVLDEPTATLTPAEVEHL 177

Query: 180 HAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGR 239
            A++  L+A+ V++I++SH L E+  +CDR TV+RDG +VA+   A+V+ A +V +MVGR
Sbjct: 178 FAVMRSLRAQGVAIIFISHHLEEIFEICDRITVLRDGAYVATCATAEVDQARLVEMMVGR 237

Query: 240 HVEF----ERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVG 295
            +E     +  K     G VVL+V  +     R  AP       F  R GEI+G AGLVG
Sbjct: 238 RIENCFPPKPAKGGEGEGEVVLEVHALQL---RRQAP----VSQFQLRRGEILGFAGLVG 290

Query: 296 AGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIR 355
           +GRT+    + GA    + ++ +   PLR   P  A+QAGI L+PE RK+QG     SI 
Sbjct: 291 SGRTETVLAMLGAHAALSCKLSMHGVPLRFADPAQALQAGIGLLPESRKEQGLITSFSIL 350

Query: 356 RNLSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGR 415
            N+SL +       G ++D R E+   E   Q++R+K   A+  +  LSGGNQQKV++ R
Sbjct: 351 HNVSLNNYGKYRLGGLFLDRRREQQATEAAMQRVRVKAPGAQVRVDTLSGGNQQKVVIAR 410

Query: 416 AMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVF 475
            +    KVLI DEPTRGID+GAK+E++Q++ +    G ++++ISSEL EV+ ++DR+ VF
Sbjct: 411 WINHAMKVLIFDEPTRGIDVGAKSEIYQLMREFTAQGYSILMISSELPEVVGMADRVCVF 470

Query: 476 REGVIVADLDAQTATEEGLMAYMATGTDRVAA 507
           R G IVA L+ +    E +M +  TG  R AA
Sbjct: 471 RGGGIVATLEGEAVNAEEIMTHATTGRIRHAA 502


Lambda     K      H
   0.320    0.136    0.380 

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: 652
Number of extensions: 39
Number of successful extensions: 8
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: 515
Length of database: 502
Length adjustment: 34
Effective length of query: 481
Effective length of database: 468
Effective search space:   225108
Effective search space used:   225108
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: 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